Application of reduced dyes in imaging

ABSTRACT

The present invention provides novel compounds and methods for hydrocyanines derived from near-infrared cyanine dyes, as reactive oxygen species probes in imaging. In certain embodiments, the present invention provides reduced dyes as substrates for ELISA and Western blots.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.14/192,827, allowed, which application is a continuation ofPCT/US2012/056739 filed Sep. 21, 2012, which application claims priorityto U.S. Provisional Application Nos. 61/538,771, filed on Sep. 23, 2011;U.S. Provisional Application No. 61/570,772, filed Dec. 14, 2011; andU.S. Provisional Application No. 61/597,677, filed Feb. 10, 2012, thedisclosures of which are hereby incorporated by reference in theirentireties for all purposes.

BACKGROUND OF THE INVENTION

Cyanine dyes have been widely used for labeling ligands or biomoleculesfor a variety of applications such as DNA sequencing. (See, for example,U.S. Pat. No. 5,571,388 for exemplary methods of identifying strands ofDNA by means of cyanine dyes.) More recently, they have been used foroptical imaging of dye-labeled biomolecules, either in vivo or in vitro.(See, for example, U.S. Pat. No. 7,597,878.) Scientists favor usingcyanine dyes in biological applications because, among other reasons,many of these dyes fluoresce in the near-infrared (NIR) region of thespectrum (600-1000 nm). This makes cyanine dyes less susceptible tointerference from autofluorescence of biomolecules.

Other advantages of cyanine dyes include, for example: 1) cyanine dyesstrongly absorb and fluoresce light; 2) many cyanine dyes do not rapidlybleach under a fluorescence microscope; 3) cyanine dye derivatives canbe made that are effective coupling reagents; 4) many structures andsynthetic procedures are available, and the class of dyes is versatile;and 5) cyanine dyes are relatively small (a typical molecular weight isabout 1,000 daltons), so they do not cause appreciable stericinterference in a way that might reduce the ability of a labeledbiomolecule to reach its binding site or carry out its function.

Hydrocyanines and deuterocyanines are a reduced form of cyanine dyes.Because of the disrupted p-conjugation, they are essentiallynonfluorescent molecules. In the presence of radicals, hydrocyanines ordeuterocyanines oxidize back to the fluorescent cyanine dyes.

Hydrocyanine and deuterocyanine dye precursors are needed for use inlabeling biomolecules as well as in vivo imaging for the diagnosis andprognosis of diseases such as cancer. Such compositions and methods areneeded for aiding in the analysis of responses to various therapies. Thepresent invention satisfies these and other needs.

BRIEF SUMMARY OF THE INVENTION

The present invention provides compounds, methods, assays and systemsrelating to hydrocyanine or deuterocyanine dyes. In certain instances,the compounds are useful for detecting reactive oxygen species (ROS)probes for in vivo applications.

As such, in one embodiment, the present invention provides a compound ofFormula I:

wherein

each R¹ is an independently selected alkyl group that is additionallysubstituted with from 0 to 1 R¹⁴ and from 0 to 1 -L-Y—Z; wherein thealkyl is optionally interrupted by at least one heteroatom;

R^(1a) is either hydrogen or deuterium;

each R^(2a) and R^(2b) is a member independently selected from the groupconsisting of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl,amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, orsulfonatoalkyl; wherein a carbon of the member is additionallysubstituted with from 0 to 1 -L-Y—Z;

each R³, R⁴, R⁵, and R⁶ is a member independently selected from thegroup consisting of hydrogen, alkyl, alkenyl, halo, hydroxyl, alkoxy,amino, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxyalkyl,carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl; wherein a carbonof the member is additionally substituted with from 0 to 1 -L-Y—Z;

-   -   R⁸, R⁹, R¹⁰, R¹¹ and R¹² are each a member independently        selected from the group consisting of hydrogen, alkyl, alkenyl,        halo, alkoxy, sulfonato, hydroxyl, amino, carboxyl,        alkoxycarbonyl, cyano, amido, thioacetyl, and -L-Y—Z; wherein at        least one member selected from the group consisting of R⁸, R⁹,        and R¹⁰ is halo;    -   each R¹³ is a member independently selected from the group        consisting of hydroxyl, amino, carboxyl, and alkoxycarbonyl;    -   each R¹⁴ is a member independently selected from the group        consisting of alkyl, alkenyl, halo, hydroxyl, alkoxy, amino,        amido, amidoalkyl, cyano, cyanoalkyl, carboxyl, alkoxycarbonyl,        amido, sulfonato, sulfonatoalkyl, thioacetyl, thioacetylalkyl,        alkoxycarbonylalkyl, and alkoxyalkyl; wherein the alkyl or        alkenyl is additionally substituted with from 0 to 1 R¹³ and        from 0 to 1 -L-Y—Z;    -   each L is an optional member independently selected from the        group consisting of a bond, a C₁-C₂₀ alkylene, and a C₁-C₂₀        alkenylene; wherein the alkylene or alkenylene is optionally        interrupted by at least one heteroatom;    -   each Y is an optional member independently selected from the        group consisting of a bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—,        —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —N(Z)—, —N(Z)C(O)—, and        —C(O)N(Z)—;    -   each Z is independently selected from the group consisting of        -L-R¹³ and -L-R¹⁶;    -   or alternatively, —Y—Z is a member selected from the group        consisting of —N(Z)₂, —N(Z)C(O)Z, and —C(O)N(Z)₂, and the two Z        groups may optionally be linked to form a cycloalkynyl group;    -   each R¹⁵ is a member independently selected from the group        consisting of alkyl and alkoxycarbonylalkyl; wherein the alkyl        is optionally interrupted by at least one heteroatom;    -   each R¹⁶ is independently a member selected from the group        consisting of activated acyl, acrylamido, optionally substituted        alkylsulfonate ester, azido, optionally substituted        arylsulfonate ester, optionally substituted amino, aziridino,        boronato, diazo, formyl, glycidyl, halo, haloacetamidyl,        haloalkyl, haloplatinato, halotriazino, hydrazinyl, imido ester,        isocyanato, isothiocyanato, maleimidyl, mercapto,        phosphoramidityl, a photoactivatable moiety, vinyl sulfonyl,        alkynyl, cycloalkynyl, cycloalkynylcarbonyl, spirocycloalkynyl,        a pegylated azido, a pegylated alkynyl, a pegylated        cycloalkynyl, a pegylated spirocycloalkynyl, an        o-diarylphosphino aryl ester, and an ortho substituted phosphine        oxide aryl ester; and    -   wherein the compound has a balanced charge.

In another embodiment, the present invention provides a compound ofFormula II:

-   -   wherein:

R¹ and R^(1a) are each independently an alkyl group that is additionallysubstituted with from 0 to 1 R¹³, wherein the alkyl is optionallyinterrupted by at least one heteroatom;

R^(1a′) and R^(1′) are each independently either hydrogen or deuterium;

each R¹³ is independently a member independently selected from the groupof hydroxyl, amino, carboxyl, alkoxycarbonyl, amido, sulfonato, andthioacetyl. In a preferred embodiment, R¹³ is carboxyl, amido, oralkoxycarbonyl;

each R¹⁴ is a member independently selected from the group of alkyl,alkenyl, halo, hydrogen, hydroxyl, alkoxy, amino, cyano, carboxyl,alkoxycarbonyl, amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl;wherein the R¹⁴ alkyl is additionally substituted with from 0 to 1 R¹³;and wherein at least one R¹⁴ is sulfonato;

L is an optional member selected from the group of a bond, a C₁-C₁₀alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene or alkenylene isoptionally interrupted by at least one heteroatom;

Y is an optional member selected from the group of a bond, —O—, —S—,—NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—,—NZC(O)—, and —C(O)NZ—;

each Z is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ and R¹⁶; wherein thealkyl is optionally interrupted by at least one heteroatom.

In still another embodiment, the present invention provides a compoundof Formula III:

wherein

R¹ is an alkyl group that is additionally substituted with from 0 to 1R¹³, and wherein the alkyl group is optionally interrupted by at leastone heteroatom;

R^(1a) is either hydrogen or deuterium;

R^(2a) and R^(2b) are each a member independently selected from thegroup of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl,amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, orsulfonatoalkyl;

R³ and R⁴ are each a member independently selected from the group ofhydrogen, alkyl, alkenyl, halo, hydroxyl, alkoxy, cyano, carboxyl,alkoxycarbonyl, amido, amino, sulfonato, alkoxyalkyl, carboxyalkyl,alkoxycarbonylalkyl, and sulfonatoalkyl;

R⁸ and R⁹ are each a member independently selected from the group ofhydrogen, alkyl, alkenyl, halo, alkoxy, sulfonato, and -L-Y—Z, whereinexactly one member selected from the group of R⁸ and R⁹ is -L-Y—Z;

R¹⁰, R¹¹, and R¹² are each a member independently selected from thegroup of hydrogen, alkyl, alkenyl, halo, alkoxy, and sulfonato;

each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl;

each R¹⁴ is a member independently selected from the group of alkyl,alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl; wherein the R¹⁴alkyl is additionally substituted with from 0 to 1 R¹³;

L is an optional member selected from the group of a bond, a C₁-C₁₀alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene or alkenylene isoptionally interrupted by at least one heteroatom;

Y is an optional member selected from the group of a bond, —O—, —S—,—NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—,—NZC(O)—, and —C(O)NZ—;

each Z is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ and R¹⁶; wherein thealkyl is optionally interrupted by at least one heteroatom;

R¹⁵ is a member selected from the group of alkyl andalkoxycarbonylalkyl; wherein the alkyl is optionally interrupted by atleast one heteroatom; and

each R¹⁶ is independently a member selected from the group of activatedacyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl, isothiocyanato,iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl, and vinylsulfonyl.

In still yet another embodiment, the present invention provides acompound of Formula IVa or IVb:

wherein

each R¹ is a member selected from the group consisting of L-Y—Z and analkyl group that is additionally substituted with from 0 to 1 R¹³ andfrom 0 to 1 R¹⁶, and wherein the alkyl is optionally interrupted by atleast one heteroatom;

R^(1a) is either hydrogen or deuterium;

each R^(2a) and R^(2b) is a member independently selected from the groupconsisting of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl,amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, orsulfonatoalkyl; wherein a carbon of the member is additionallysubstituted with from 0 to 1 R¹⁶;

each R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) is a memberindependently selected from the group consisting of hydrogen, alkyl,alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, andsulfonatoalkyl, wherein a carbon of the member is additionallysubstituted with from 0 to 1 R¹⁶;

R⁸, R⁹, R¹⁰, R¹¹ and R¹² are each a member independently selected fromthe group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy,sulfonato, sulfonatoalkyl, hydroxyl, amino, carboxyl, alkoxycarbonyl,cyano, amido, thioacetyl, and -L-Y—Z; wherein, at least one memberselected from the group consisting of R⁸, R⁹, and R¹⁰ is -L-Y—Z;

each L is an optional member independently selected from the groupconsisting of a bond, a C₁-C₂₀ alkylene, and a C₁-C₂₀ alkenylene;wherein the alkylene or alkenylene is optionally interrupted by at leastone heteroatom;

each Y is an optional member independently selected from the groupconsisting of a bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—,—NR¹⁵C(O)—, —C(O)NR¹⁵—, —N(Z)—, —N(Z)C(O)—, and —C(O)N(Z)—;

each Z is independently selected from the group consisting of -L-R¹³ and-L-R¹⁶;

each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl;

each R¹⁵ is a member independently selected from the group consisting ofalkyl and alkoxycarbonylalkyl; wherein the alkyl is optionallyinterrupted by at least one heteroatom;

each R¹⁶ is independently a member selected from the group consisting ofactivated acyl, acrylamido, optionally substituted alkylsulfonate ester,azido, optionally substituted arylsulfonate ester, optionallysubstituted amino, aziridino, boronato, cycloalkynyl,cycloalkynylcarbonyl, diazo, formyl, glycidyl, halo, haloacetamidyl,haloalkyl, haloplatinato, halotriazino, hydrazinyl, imido ester,isocyanato, isothiocyanato, maleimidyl, mercapto, phosphoramidityl, aphotoactivatable moiety, vinyl sulfonyl, alkynyl, a pegylated azido, apegylated alkynyl, a pegylated cycloalkynyl, an ortho substitutedphosphinyl aryl ester (e.g., TPPME), a spirocycloalkynyl, and an orthosubstituted phosphine oxide aryl ester.

In still yet another embodiment, the present invention provides acompound of Formula V:

wherein:

each R¹ is a member selected from the group consisting of L-Y—Z and analkyl group that is additionally substituted with from 0 to 1 R¹³ andfrom 0 to 1 R¹⁶, wherein the alkyl is optionally interrupted by at leastone heteroatom;

R^(1a) is either hydrogen or deuterium;

each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl. In apreferred embodiment, R¹³ is carboxyl, amido, or alkoxycarbonyl;

L is an optional member selected from the group of a bond, a C₁-C₁₀alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene or alkenylene isoptionally interrupted by at least one heteroatom;

Y is an optional member selected from the group of a bond, —O—, —S—,—NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—,—NZC(O)—, and —C(O)NZ—;

each Z is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ and R¹⁶; wherein thealkyl is optionally interrupted by at least one heteroatom;

R¹⁵ is a member selected from the group of alkyl andalkoxycarbonylalkyl, wherein the alkyl is optionally interrupted by atleast one heteroatom; and

each R¹⁶ is independently a member selected from the group of activatedacyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl, isothiocyanato,iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl, and vinylsulfonyl.

These and other objects, advantages and embodiments will become moreapparent when read with the accompanying figures and detaileddescription which follow.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 demonstrates the usefulness of the hydrocyanine dye analog toIRIR-780780 as an HRP substrate. The wells from 01 to 12 show thefluorescence with decreasing HRP-enzyme concentrations (from 800 nM to0.8 nM).

FIG. 2 shows an NIR HRP substrate in a direct ELISA assay using rabbitimmunoglobulin G (IgG) as antigen and goat anti-rabbit HRP as thedetection antibody.

FIG. 3 illustrates the efficacies of D-IR780F2 as an 800 HRP substratein an ELISA format.

FIG. 4A-B show representative examples of ROS imaging by H-Cy3 (FIG. 4A)and H-IR780F2 (FIG. 4B). Both H-Cy3 and H-IR780F2 showed increasedfluorescent intensity in the LPS treated cells compared to the untreatedcells.

FIG. 5 shows a synthetic route for the preparation of H/D-IR650 diol.

FIG. 6 shows a synthetic route to H-IRDye® 800CW from the correspondingcyanine.

FIG. 7 shows detection of oxygen species (ROS) in untreated mousemacrophage cells (RAW 264.7; left panel) and RAW 264.7 cells treatedwith lipopolysaccharide endotoxin (LPS; right panel). After LPStreatment, cells were loaded with H-IR650DIOL and imaged viafluorescence microscopy.

FIG. 8 shows detection of ROS in untreated RAW cells (left panels) andRAW cells treated with lipopolysaccharide endotoxin (LPS; right panels).After LPS treatment, cells were loaded with H-IR680DIOL (10 μM, toppanels; 50 μM, bottom panels) and imaged via fluorescence microscopy.

FIG. 9 shows detection of ROS in untreated RAW cells (left panels) andRAW cells treated with lipopolysaccharide endotoxin (LPS; right panels).After LPS treatment, cells were loaded with H-Cy5 and imaged viafluorescence microscopy.

FIG. 10 shows detection of ROS RAW cells treated with varying amounts ofhydrogen peroxide (0 mM, top panel; 0.1 mM, middle panel; 1 mM, bottompanel). Cells were loaded with H-IR675 prior to peroxide treatment andimaging via fluorescence microscopy

FIG. 11 shows detection of ROS in untreated RAW cells (left panels) andRAW cells treated with hydrogen peroxide (right panels). Cells wereloaded with H-Cy3 prior to peroxide treatment and imaging viafluorescence microscopy.

FIG. 12 shows detection of ROS RAW cells treated with varying amounts ofhydrogen peroxide (0 mM, left panel; 0.1 mM, center panel; 1 mM, rightpanel). Cells were loaded with H-IR780F2 prior to peroxide treatment andimaging via fluorescence microscopy.

FIG. 13 shows detection of ROS RAW cells treated with varying amounts ofepidermal growth factor (EGF; 0 ng/mL, left panel; 20 ng/mL, centerpanel; 100 ng/mL, right panel). Cells were loaded with H-IR780F2 priorto EGF treatment and imaging via fluorescence microscopy.

FIG. 14 shows a schematic representation of the immunoassay methods ofthe present invention.

FIG. 15A-D show the immunoassay analysis of cell lysates using variousfluorescent probes. 4-12% Bis-Tris gels were loaded A431 lysate samples,electrophoresed, transferred to nitrocellulose membranes, and blocked.The blots were probed with mouse anti-β actin antibodies followed by HRPgoat anti-mouse antibodies (FIGS. 15A-B) or cyanine-antibody conjugates(FIGS. 15C-D). FIGS. 15A-B were incubated for 5 min withchemifluorescent substrate after antibody binding: (FIG. 15A) 10 μMH-IR780F2 (200 μM H₂O₂, pH 5.0 Citrate buffer); (FIG. 15B) HRP 680 ELISAsubstrate (LI-COR). FIG. 15C and FIG. 15D were incubated with IRDye800CW GAM and IRDye 680RD GAM, respectively, after binding of mouseanti-β actin antibodies.

FIG. 16A-B show the immunoassay analysis of biological samples using(FIG. 16A) chemifluorescent substrate H-IR780F2 (top and middle panels),as compared to fluroscently-labeled antibodies (bottom left panel) andchemiluminescent reagents (bottom right panel); (FIG. 16B) shows aquantitative comparison of two duplicate Western blots using H-IR780F2(B=red and D=blue).

DETAILED DESCRIPTION I. Definitions

The terms “a,” “an,” or “the” as used herein not only include aspectswith one member, but also include aspects with more than one member. Forexample, an embodiment of a method of imaging that comprises using acompound set forth herein would include an aspect in which the methodcomprises using two or more compounds set forth herein.

The term “about” as used herein to modify a numerical value indicates adefined range around that value. If “X” were the value, “about X” wouldindicate a value from 0.9X to 1.1X, and more preferably, a value from0.95X to 1.05X. Any reference to “about X” specifically indicates atleast the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X, 1.01X, 1.02X,1.03X, 1.04X, and 1.05X. Thus, “about X” is intended to teach andprovide written description support for a claim limitation of, e.g.,“0.98X.”

When the quantity “X” only allows whole-integer values (e.g., “Xcarbons”) and X is at most 15, “about X” indicates from (X−1) to (X+1).In this case, “about X” as used herein specifically indicates at leastthe values X, X−1, and X+1. If X is at least 16, the values of 0.90X and1.10X are rounded to the nearest whole-integer values to define theboundaries of the range.

When the modifier “about” is applied to describe the beginning of anumerical range, it applies to both ends of the range. Thus, “from about700 to 850 nm” is equivalent to “from about 700 nm to about 850 nm.”When “about” is applied to describe the first value of a set of values,it applies to all values in that set. Thus, “about 680, 700, or 750 nm”is equivalent to “about 680 nm, about 700 nm, or about 750 nm.” However,when the modifier “about” is applied to describe only the end of therange or only a later value in the set of values, it applies only tothat value or that end of the range. Thus, the range “about 2 to 10” isthe same as “about 2 to about 10,” but the range “2 to about 10” is not.

“Activated acyl” as used herein includes a —C(O)-LG group. “Leavinggroup” or “LG” is a group that is susceptible to displacement by anucleophilic acyl substitution (i.e., a nucleophilic addition to thecarbonyl of —C(O)-LG, followed by elimination of the leaving group).Representative leaving groups include halo, cyano, azido, carboxylicacid derivatives such as t-butylcarboxy, and carbonate derivatives suchas i-BuOC(O)O—. An activated acyl group may also be an activated esteras defined herein or a carboxylic acid activated by a carbodiimide toform an anhydride or mixed anhydride —OC(O)R^(a) or —OC(NR^(a))NHR^(b),wherein R^(a) and R^(b) are members independently selected from thegroup consisting of C₁-C₆ alkyl, C₁-C₆ perfluoroalkyl, C₁-C₆ alkoxy,cyclohexyl, 3-dimethylaminopropyl, N-morpholinoethyl or aryl. Preferredactivated acyl groups include activated esters.

“Activated ester” as used herein includes a derivative of a carboxylgroup that is more susceptible to displacement by nucleophilic additionand elimination than an ethyl ester group (e.g., an NHS ester, asulfo-NHS ester, a PAM ester, or a halophenyl ester). Representativecarbonyl substituents of activated esters include succinimidyloxy(—OC₄H₄NO₂), sulfosuccinimidyloxy (—OC₄H₃NO₂SO₃H), -1-oxybenzotriazolyl(—OC₆H₄N₃); 4-sulfo-2,3,5,6-tetrafluorophenyl; or an aryloxy group thatis optionally substituted one or more times by electron-withdrawingsubstituents such as nitro, fluoro, chloro, cyano, trifluoromethyl, orcombinations thereof (e.g., pentafluorophenyloxy). Preferred activatedesters include succinimidyloxy and sulfosuccinimidyloxy esters.

“Acyl” as used herein includes an alkanoyl, aroyl, heterocycloyl, orheteroaroyl group as defined herein. Representative acyl groups includeacetyl, benzoyl, nicotinoyl, and the like.

“Alkanoyl” as used herein includes an alkyl-C(O)— group wherein thealkyl group is as defined herein. Representative alkanoyl groups includeacetyl, ethanoyl, and the like.

“Alkenyl” as used herein includes a straight or branched aliphatichydrocarbon group of 2 to about 15 carbon atoms that contains at leastone carbon-carbon double bond. Preferred alkenyl groups have 2 to about12 carbon atoms. More preferred alkenyl groups contain 2 to about 6carbon atoms. “Lower alkenyl” as used herein includes alkenyl of 2 toabout 6 carbon atoms. Representative alkenyl groups include vinyl,allyl, n-butenyl, 2-butenyl, 3-methylbutenyl, n-pentenyl, heptenyl,octenyl, decenyl, and the like.

“Alkenylene” as used herein includes a straight or branched bivalenthydrocarbon chain containing at least one carbon-carbon double or triplebond. Preferred alkenylene groups include from 2 to about 12 carbons inthe chain, and more preferred alkenylene groups include from 2 to 6carbons in the chain. In one aspect, hydrocarbon groups that contain acarbon-carbon double bond are preferred. In a second aspect, hydrocarbongroups that contain a carbon-carbon triple bond are preferred.Representative alkenylene groups include —CH═CH—, —CH₂—CH═CH—,—C(CH₃)═CH—, —CH₂CH═CHCH₂—, ethynylene, propynylene, n-butynylene, andthe like.

“Alkoxy” as used herein includes an alkyl-O— group wherein the alkylgroup is as defined herein. Representative alkoxy groups includemethoxy, ethoxy, n-propoxy, i-propoxy, n-butoxy, heptoxy, and the like.

“Alkoxyalkyl” as used herein includes an alkyl-O-alkylene- group whereinalkyl and alkylene are as defined herein. Representative alkoxyalkylgroups include methoxyethyl, ethoxymethyl, n-butoxymethyl andcyclopentylmethyloxyethyl.

“Alkoxycarbonyl” as used herein includes an ester group; i.e., analkyl-O—CO— group wherein alkyl is as defined herein. Representativealkoxycarbonyl groups include methoxycarbonyl, ethoxycarbonyl,t-butyloxycarbonyl, and the like.

“Alkoxycarbonylalkyl” as used herein includes an alkyl-O—CO-alkylene-group wherein alkyl and alkylene are as defined herein. Representativealkoxycarbonylalkyl include methoxycarbonylmethyl, ethoxycarbonylmethyl,methoxycarbonylethyl, and the like.

“Alkyl” as used herein includes an aliphatic hydrocarbon group, whichmay be straight or branched-chain, having about 1 to about 20 carbonatoms in the chain. Preferred alkyl groups have 1 to about 12 carbonatoms in the chain. More preferred alkyl groups have 1 to 10 or 1 to 6carbon atoms in the chain. “Branched-chain” as used herein includes thatone or more lower alkyl groups such as methyl, ethyl or propyl areattached to a linear alkyl chain (e.g., 2-methylbutyl). “Lower alkyl” asused herein includes 1 to about 6 carbon atoms, preferably 5 or 6 carbonatoms in the chain, which may be straight or branched. Representativealkyl groups include methyl, ethyl, n-propyl, isopropyl, n-butyl,t-butyl, n-pentyl, and 3-pentyl.

“Alkylene” as used herein includes a straight or branched bivalenthydrocarbon chain of 1 to about 6 carbon atoms. Preferred alkylenegroups are the lower alkylene groups having 1 to about 4 carbon atoms.Representative alkylene groups include methylene, ethylene, and thelike.

“Alkylsulfonate ester” as used herein includes an alkyl-SO₃— groupwherein the alkyl group is as defined herein. Preferred alkylsulfonateester groups are those wherein the alkyl group is lower alkyl.Representative alkylsulfonate ester groups include mesylate ester (i.e.,methylsulfonate ester).

An “optionally substituted” alkylsulfonate ester includes analkylsulfonate ester as defined herein, wherein the aryl group isadditionally substituted with from 0 to 3 halo, alkyl, aryl, haloalkyl,or haloaryl groups as defined herein. Preferred optionally substitutedalkylsulfonate groups include triflate ester (i.e.,trifluoromethylsulfonate ester).

“Alkylthio” as used herein includes an alkyl-S— group wherein the alkylgroup is as defined herein. Preferred alkylthio groups are those whereinthe alkyl group is lower alkyl. Representative alkylthio groups includemethylthio, ethylthio, isopropylthio, heptylthio, and the like.

“Alkylthioalkyl” as used herein includes an alkylthio-alkylene- groupwherein alkylthio and alkylene are defined herein. Representativealkylthioalkyl groups include methylthiomethyl, ethylthiopropyl,isopropylthioethyl, and the like.

“Alkynyl” as used herein includes a straight or branched aliphatichydrocarbon group of 2 to about 15 carbon atoms that contains at leastone carbon-carbon triple bond. Preferred alkynyl groups have 2 to about12 carbon atoms. More preferred alkynyl groups contain 2 to about 6carbon atoms. “Lower alkynyl” as used herein includes alkynyl of 2 toabout 6 carbon atoms. Representative alkynyl groups include propynyl,2-butynyl, 3-methylbutynyl, n-pentynyl, heptynyl, and the like.

“Amido” as used herein includes a group of formula Y₁Y₂N—C(O)— whereinY₁ and Y₂ are independently hydrogen, alkyl, or alkenyl; or Y₁ and Y₂,together with the nitrogen through which Y₁ and Y₂ are linked, join toform a 4- to 7-membered azaheterocyclyl group (e.g., piperidinyl).Representative amido groups include primary amido (H₂N—C(O)—),methylamido, dimethylamido, diethylamido, and the like. Preferably,“amido” is an —C(O)NRR′ group where R and R′ are members independentlyselected from the group consisting of H and alkyl. More preferably, atleast one of R and R′ is H.

“Amidoalkyl” as used herein includes an amido-alkylene- group whereinamido and alkylene are defined herein. Representative amidoalkyl groupsinclude amidomethyl, amidoethyl, dimethylamidomethyl, and the like.

“Amino” as used herein includes a group of formula Y₁Y₂N— wherein Y₁ andY₂ are independently hydrogen, acyl, aryl, or alkyl; or Y₁ and Y₂,together with the nitrogen through which Y₁ and Y₂ are linked, join toform a 4- to 7-membered azaheterocyclyl group (e.g., piperidinyl).Optionally, when Y₁ and Y₂ are independently hydrogen or alkyl, anadditional substituent can be added to the nitrogen, making a quaternaryammonium ion. Representative amino groups include primary amino (H₂N—),methylamino, dimethylamino, diethylamino, tritylamino, and the like.Preferably, “amino” is an —NRR′ group where R and R′ are membersindependently selected from the group consisting of H and alkyl.Preferably, at least one of R and R′ is H.

An “optionally substituted” amino group includes an amino group asdefined herein.

“Aminoalkyl” as used herein includes an amino-alkylene- group whereinamino and alkylene are defined herein. Representative aminoalkyl groupsinclude aminomethyl, aminoethyl, dimethylaminomethyl, and the like.

“Aroyl” as used herein includes an aryl-CO— group wherein aryl isdefined herein. Representative aroyl include benzoyl, naphth-1-oyl andnaphth-2-oyl.

“Aryl” as used herein includes an aromatic monocyclic or multicyclicring system of 6 to about 14 carbon atoms, preferably of 6 to about 10carbon atoms. Representative aryl groups include phenyl and naphthyl.

“Arylsulfonate ester” as used herein includes an aryl-SO₃— group whereinthe aryl group is as defined herein. Representative arylsulfonate estergroups include phenylsulfonate ester.

An “optionally substituted” arylsulfonate ester includes anarylsulfonate ester as defined herein, wherein the aryl group isadditionally substituted with from 0 to 3 halo, alkyl, aryl, haloalkyl,or haloaryl groups as defined herein. Preferred optionally substitutedarylsulfonate esters include tosylate ester (i.e., p-tolylsulfonateester).

“Aromatic ring” as used herein includes 5-12 membered aromaticmonocyclic or fused polycyclic moieties that may include from zero tofour heteroatoms selected from the group consisting of oxygen, sulfur,selenium, and nitrogen. Exemplary aromatic rings include benzene,pyrrole, furan, thiophene, imidazole, oxazole, thiazole, triazole,pyrazole, pyridine, pyrazine, pyridazine, pyrimidine, naphthalene,benzathiazoline, benzothiophene, benzofurans, benzimidazole, indole,benzindole, quinoline, and the like. The aromatic ring group can besubstituted at one or more positions with halo, alkyl, alkoxy, alkoxycarbonyl, haloalkyl, cyano, sulfonato, amino sulfonyl, aryl, sulfonyl,aminocarbonyl, carboxy, acylamino, alkyl sulfonyl, amino and substitutedor unsubstituted substituents.

“Balanced charge” as used herein includes the condition that the netcharge for a compound and its associated counterions be zero understandard physiological conditions. In order to achieve a balancedcharge, a skilled person will understand that after the first additionalsulfonato group that balances the +1 charge of the indolinium ring, acationic counterion (e.g., the cation of a Group I metal such as sodium)must be added to balance the negative charge from additional sulfonatogroups. Similarly, anionic counterions must be added to balance anyadditional cationic groups (e.g., most basic amino groups underphysiological conditions). In some embodiments, a counterion can becovalently connected to the compound (e.g., a zwitterionic groupcontaining a sulfonato-anionic group and a trialkylamino cationicgroup).

“Biomolecule” as used herein includes a natural or synthetic moleculefor use in biological systems. Preferred biomolecules include a protein,a peptide, an enzyme substrate, a hormone, an antibody, an antigen, ahapten, an avidin, a streptavidin, a carbohydrate, a carbohydratederivative, an oligosaccharide, a polysaccharide, a nucleic acid, adeoxynucleic acid, a fragment of DNA, a fragment of RNA, nucleotidetriphosphates, acyclo terminator triphosphates, PNA, and the like. Morepreferred biomolecules include a protein, a peptide, an antibody, anavidin, a streptavidin, and the like. Even more preferred biomoleculesinclude a peptide, an antibody, an avidin, and a streptavidin.

“Carboxy” and “carboxyl” as used herein include a HOC(O)— group (i.e., acarboxylic acid) or a salt thereof. Preferably, the salt counterion isnon-toxic (e.g., a cation commonly used in pharmaceuticals).Representative salts include an alkali metal salt (e.g., sodium,potassium) or a tetraalkylammonium salt (e.g., tetraethylammonium),

“Carboxyalkyl” as used herein includes a HOC(O)-alkylene- group whereinalkylene is defined herein. Representative carboxyalkyls includecarboxymethyl (i.e., HOC(O)CH₂—) and carboxyethyl (i.e., HOC(O)CH₂CH₂—).

“Cycloalkenyl” as used herein includes a cyclic hydrocarbon group of 4to about 15 carbon atoms that contains at least one carbon-carbon doublebond. The cycloalkenyl ring may include from 0 to 6 R¹⁴ substituents(e.g., R¹⁴ as defined in Formula I) and 0 to 2 R^(L) substituents, andwhen present, the ring-fused aryl or heteroaryl rings may also includefrom 0 to 4 R¹⁴ substituents and 0 to 2 R^(L) substituents. Preferredalkenyl groups have 5 to about 12 carbon atoms. More preferred alkenylgroups contain 7 to about 14 carbon atoms. Representative cycloalkenylgroups include cyclopentenyl, cyclohexenyl, and the like.

“Cycloalkynyl” as used herein includes a mono- or multicyclichydrocarbon ring system of 5 to about 15 carbon atoms that contains atleast one carbon-carbon triple bond. In a preferred aspect, the cyclichydrocarbon may optionally be interrupted by a heteroatom (e.g., N, O,S; preferably N) and may include at least one ring-fused aryl orheteroaryl ring (e.g., DBCO or DBCO-1). The cycloalkynyl ring mayinclude from 0 to 6 R¹⁴ substituents (e.g., R¹⁴ as defined in Formula I)and 0 to 2 R^(L) substituents, and when present, the ring-fused aryl orheteroaryl rings may also include from 0 to 4 R¹⁴ substituents and 0 to2 R^(L) substituents. In some aspect, the R^(L) substituent includes aring-fused heteroaryl group as part of the linking group with thebiomolecule (e.g., the reaction of DBCO with an azide-substitutedbiomolecule). Preferred alkynyl groups have 5 to about 12 carbon atoms.More preferred alkynyl groups contain 7 to about 14 carbon atoms.Representative cycloalkynyl groups include cyclopentynyl, cyclohexynyl,cyclooctynyl, dibenzocyclooctynyl (or DBCO, which includes a nitrogen inthe “octyne” ring or DBCO-1), BARAC, DIFO, DIBO, TMDIBO, DIFO3 and thelike.

“Cycloalkynylcarbonyl” includes the definition of cycloalkynyl abovewith an exocylic carbonyl, for example, a dibenzocyclooctynylcarbonyl orC(O)DBCO, which includes a nitrogen in the “octyne” ring and anexocyclic carbonyl group, and the like.

“Cycloalkyl” as used herein includes a non-aromatic mono- or multicyclicring system of about 3 to about 10 carbon atoms, preferably of about 5to about 10 carbon atoms. More preferred cycloalkyl rings contain 5 or 6ring atoms. A cycloalkyl group optionally comprises at least onesp²-hybridized carbon (e.g., a ring incorporating an endocyclic orexocyclic olefin). Representative monocyclic cycloalkyl groups includecyclopentyl, cyclohexyl, cyclohexenyl, cycloheptyl, and the like.Representative multicyclic cycloalkyl include 1-decalin, norbornyl,adamantyl, and the like.

“Cycloalkylene” as used herein includes a bivalent cycloalkyl havingabout 4 to about 8 carbon atoms. Preferred cycloalkylenyl groups include1,2-, 1,3-, or 1,4-cis- or trans-cyclohexylene.

“Cyanine dye” as used herein includes a compound having two substitutedor unsubstituted nitrogen-containing heterocyclic rings joined by anunsaturated bridge. In certain instances, cyanine dyes are referred toherein as “oxidized” dyes. After reduction (by hydrogen or deuterium),the cyanine dyes are reduced to compounds of a preferred embodiment ofthe present invention (i.e., hydrocyanines). For example, “reducedcyanine dye,” “hydrocyanine,” or “deuterocyanine” include a cyanine dyewherein the iminium cation has been reduced.

“Exocyclic alkene” or “exocyclic olefin” as used interchangeably hereininclude an alkene having one alkene carbon that is part of a ring andthe other alkene carbon not part of the same ring, though it may beincluded within a second ring. The second alkene carbon can beunsubstituted or substituted. If the second alkene carbon isdisubstituted, the substituents can be the same (e.g., 1,1-dimethylsubstitution) or different (e.g., 1-methyl-1-(2-ethoxyethyl)substitution). Examples of compounds with exocyclic alkenes includemethylenecyclohexane; (E)-1-ethylidene-2,3-dihydro-1H-indene;pentan-3-ylidenecycloheptane; 2-cyclobutylidenepropan-1-ol; and(3-methoxycyclopent-2-enylidene)cyclohexane.

“Geminal” substituents as used herein includes two or more substituentsthat are directly attached to the same atom. An example is 3,3-dimethylsubstitution on a cyclohexyl or spirocyclohexyl ring.

“Halo” or “halogen” as used herein include fluoro, chloro, bromo, oriodo.

“Haloalkyl” as used herein includes an alkyl group wherein the alkylgroup includes one or more halo-substituents (e.g., trifluoromethyl).

“Haloaryl” as used herein includes an alkyl group wherein the aryl groupincludes one or more halo-substituents (e.g., 2,4,6-phenyl).

“Heptamethine” as used herein includes a polymethine containing sevenpolymethine carbons. In a preferred embodiment, the heptamethine issubstituted at the 4-position.

“Heteroatom” as used herein includes an atom other than carbon orhydrogen. Representative heteroatoms include O, S, P, and N. Thenitrogen or sulfur atom of the heteroatom is optionally oxidized to thecorresponding N-oxide, S-oxide (sulfoxide), or S,S-dioxide (sulfone). Ina preferred aspect, a heteroatom has at least two bonds to alkylenecarbon atoms (e.g., —C₁-C₉ alkylene-O—C₁-C₉ alkylene-). In someembodiments, a heteroatom is further substituted with an acyl, alkyl,aryl, cycloalkyl, heterocyclyl, or heteroaryl group (e.g., —N(Me)-;—N(Ac)—).

“Heteroaroyl” as used herein includes a heteroaryl-C(O)— group whereinheteroaryl is as defined herein. Representative heteroaroyl groupsinclude thiophenoyl, nicotinoyl, pyrrol-2-ylcarbonyl, pyridinoyl, andthe like.

“Heterocycloyl” as used herein includes a heterocyclyl-C(O)— groupwherein heterocyclyl is as defined herein. Representative heterocycloylgroups include N-methyl prolinoyl, tetrahydrofuranoyl, and the like.

“Heterocyclyl” as used herein includes a non-aromatic saturatedmonocyclic or multicyclic ring system of about 3 to about 10 ring atoms,preferably about 5 to about 10 ring atoms, in which one or more of theatoms in the ring system is an element or elements other than carbon,e.g., nitrogen, oxygen or sulfur. Preferred heterocyclyl groups containabout 5 to about 6 ring atoms. A heterocyclyl group optionally comprisesat least one sp²-hybridized atom (e.g., a ring incorporating ancarbonyl, endocyclic olefin, or exocyclic olefin). The prefix “aza,”“oxa,” or “thia” before heterocyclyl means that at least a nitrogen,oxygen or sulfur atom respectively is present as a ring atom. Thenitrogen or sulfur atom of the heterocyclyl is optionally oxidized tothe corresponding N-oxide, S-oxide or S,S-dioxide. Representativemonocyclic heterocyclyl rings include piperidyl, pyrrolidinyl,piperazinyl, morpholinyl, thiomorpholinyl, thiazolidinyl,1,3-dioxolanyl, 1,4-dioxanyl, tetrahydrofuranyl, tetrahydrothiophenyl,tetrahydrothiopyranyl, and the like.

“Heterocyclylene” as used herein includes a bivalent heterocyclyl group.Representative cycloalkylenyl groups include 1,2-, 1,3-, or1,4-piperdinylene as well as 2,3- or 2,4-cis- or trans-piperidinylene.

“Heteroaryl” as used herein includes an aromatic monocyclic ormulticyclic ring system of about 5 to about 14 ring atoms, preferablyabout 5 to about 10 ring atoms, in which at least one of the atoms inthe ring system is an element other than carbon, i.e., nitrogen, oxygenor sulfur. In one embodiment, preferred heteroaryls contain an aromaticring with about 5 to about 6 ring atoms. The prefix “aza,” “oxa,” or“thia” before heteroaryl means that at least a nitrogen, oxygen orsulfur atom respectively is present as a ring atom. A nitrogen atom of aheteroaryl is optionally oxidized to the corresponding N-oxide.Representative heteroaryls include pyrazinyl, furanyl, thienyl, pyridyl,pyrimidinyl, isoxazolyl, isothiazolyl, oxazolyl, thiazolyl, pyrazolyl,furazanyl, pyrrolyl, pyrazolyl, triazolyl, 1,2,4-thiadiazolyl,pyrazinyl, pyridazinyl, quinoxalinyl, phthalazinyl,imidazo[1,2-a]pyridine, imidazo[2,1-b]thiazolyl, benzofurazanyl,indolyl, azaindolyl, benzimidazolyl, benzothienyl, quinolinyl,imidazolyl, thienopyridyl, quinazolinyl, thienopyrimidyl,pyrrolopyridyl, imidazopyridyl, isoquinolinyl, benzoazaindolyl,1,2,4-triazinyl, benzothiazolyl and the like.

“Hydroxyalkyl” as used herein includes an alkyl group as defined hereinsubstituted with one or more hydroxy groups. Preferred hydroxyalkylscontain lower alkyl. Representative hydroxyalkyl groups includehydroxymethyl and 2-hydroxyethyl.

When any two substituent groups or any two instances of the samesubstituent group are “independently selected” from a list ofalternatives, they may be the same or different. For example, if R^(a)and R^(b) are independently selected from the group consisting ofmethyl, hydroxymethyl, ethyl, hydroxyethyl, and propyl, then a moleculewith two R^(a) groups and two R^(b) groups could have all groups bemethyl. Alternatively, the first R^(a) could be methyl, the second R^(a)could be ethyl, the first R^(b) could be propyl, and the second R^(b)could be hydroxymethyl (or any other substituents taken from the group).Alternatively, both R^(a) and the first R^(b) could be ethyl, while thesecond R^(b) could be hydroxymethyl (i.e., some pairs of substituentgroups may be the same, while other pairs may be different).

“Linking group” as used herein includes the atoms joining a dye compound(e.g., a dye selected from the examples or the dyes of Formula I-VII)with a biomolecule. Table 1 includes a list of preferred bonds forlinking groups (i.e., Column C); the linking group comprises theresulting bond and optionally can include additional atoms. See also R.Haugland, Molecular Probes Handbook of Fluorescent Probes and ResearchChemicals, Molecular Probes, Inc. (1992). In one embodiment, R¹⁶represents a linking group precursor before the attachment reaction witha biomolecule, and R^(L) represents the resultant attachment between thecompound of Formula I-VII and the biomolecule (i.e., R^(L) comprises thelinking group and the biomolecule linked thereby). In one embodiment,preferred reactive funtionalities include phosphoramidite groups, anactivated ester (e.g., an NHS ester), thiocyanate, isothiocyanate,maleimide, and iodoacetamide.

“Methine carbon” or “polymethine carbon” as used herein include a carbonthat is directly connecting the two heterocyclic rings by means of thepolymethine bridge. In a preferred embodiment, at least one polymethinecarbon of a polymethine bridge is additionally substituted with anothergroup such as alkyl, cycloalkyl, or aryl (e.g., —CH═CH—C(Ar)═CH—CH═ or═CH—CH═C(Ar)—(CH═CH)₂—).

The “oxidized form” of a compound is a compound in its “oxidized state.”This designates a compound of formula X (preferably, a fluorescentcompound) as opposed to its reduced form of formula (X+2^(e−)+2M⁺),wherein M⁺ is preferably H⁺. For example, reaction of a compound ofFormula I with an oxidant produces a fluorescent, oxidized form byabstraction of the R_(1a) hydrogen or hydrogen isotope (i.e., the lossof H⁻ and a cationic counterion).

“Pentamethine” as used herein includes a polymethine containing fivepolymethine carbons. In a preferred embodiment, the pentamethine issubstituted at the 3-position.

A “photoactivatable moiety” is a chemical group or molecule that, uponexposure to light, absorbs a photon to enter an excited state. Theexcited-state group or molecule undergoes a chemical reaction or seriesof reactions. Alternatively, the excitation changes the light-emittingproperties of the group or molecules (e.g., photoactivatable fluorescentdyes). Examples of photoactivatable moieties include aryl azides,benzophenones (e.g., 4-benzoyloxybenzoic acid as well as its esters andamides), nitroaryl groups (e.g., 5-carboxymethoxy-2-nitrobenzyl (CMNB);α-carboxy-2-nitrobenzyl (CNB); 4,5-dimethoxy-2-nitrobenzyl (DMNB);1-(4,5-dimethoxy-2-nitrophenyl)ethyl (DMNPE); nitrophenyl (NP); and1-(2-nitrophenyl)ethyl (NPE) groups), coumarins, diazo groups,photoactivatable fluorescent dyes (e.g.,5-carboxyfluorescein-bis-(5-carboxymethoxy-2-nitrobenzyl) ether,β-alanine-carboxamide, succinimidyl ester), and tetrazoles.

“Polyene” as used herein includes a straight or branched bivalenthydrocarbon chain containing at least two “alkenylene” groups as definedherein that are in conjugation. The polyene is optionally substitutedwith one or more “alkylene group substituents” as defined herein (i.e.,in the Examples and disclosed embodiments). A portion of the polyene maybe incorporated into a ring (i.e., ═C(R)—, wherein R and the terminalbond are linked in a larger ring; or —C(R¹)═C(R²)—, wherein R¹ and R²are linked in a larger ring). Representative polyenes include—CH═CH—CH═CH—, —CH═CH—C(Ar)═CH—CH═C(R)—, —C(R)═CH—CH═C(Ar)—(CH═CH)₂—,and the like.

“Polymethine” or “polymethine bridge” as used herein includes the seriesof conjugated, sp²-hybridized carbons that form the unsaturated bridgedirectly connecting the two nitrogen-containing heterocyclic rings of adye compound (e.g., a fluorescent compound of Formula I-VII). In apreferred embodiment, the polymethine has five or seven carbons directlyconnecting the heterocyclic rings (i.e., pentamethine or heptamethine).

“Phosphoramidityl” as used herein includes a trivalent phosphorous atombonded to two alkoxy groups and an amino group.

As used herein, “reduced dye” includes a dye molecule in which one ormore π-bonds have been reduced, disrupting the extended π-conjugation,resulting in a molecule that exhibits negligible or no fluorescence atnear-IR frequencies or substantially non-fluorescent. For example,“reduced cyanine dye,” “hydrocyanine,” or “deuterocyanine” include acyanine dye wherein the iminium cation has been reduced.“Deuterocyanine,” as used herein, includes a cyanine dye that has beenreduced by a deuterated reducing agent thus incorporating deuterium intothe reduced molecule.

As used herein, “reactive oxygen species” and “ROS” referinterchangeably to molecules or ions that contain oxygen ions, freeradicals, peroxides, or combinations thereof. Reactive oxygen speciescan be organic or inorganic. Examples of reactive oxygen speciesinclude, but are not limited to, super oxides; oxygen free radicals,such as hydroxyl radicals and peroxyl radicals; peroxides, singletoxygen, ozone, nitrogen monoxide; anions, such as hydroxyl anions andsuperoxide anions; hypochlorus acid; and peroxynitrites, as well ascombinations of any such reactive oxygen species.

“Sulfonato” as used herein includes an —SO₃ ⁻ group, preferably balancedby a cation such as H⁺, Na⁺, K⁺, and the like. Preferably, the cation isnon-toxic (e.g., a cation commonly used in pharmaceuticals).Representative cations include an alkali metal ion (e.g., sodium,potassium) or a tetraalkylammonium (e.g., tetraethylammonium),

“Sulfonatoalkyl” as used herein includes an sulfonato-alkylene- groupwherein sulfonato and alkylene are as defined herein. A more preferredembodiment includes alkylene groups having from 2 to 6 carbon atoms, anda most preferred embodiment includes alkylene groups having 2, 3, or 4carbons. Representative sulfonatoalkyls include sulfonatomethyl,3-sulfonatopropyl, 4-sulfonatobutyl, 5-sulfonatopentyl,6-sulfonatohexyl, and the like.

As used herein, the term “ionic group” includes a moiety comprising oneor more charged substituents. The “charged substituent” is a functionalgroup that is generally anionic or cationic when in substantiallyneutral aqueous conditions (e.g., a pH of about 6.5 to 8.0 or aboutphysiological pH (7.4)). As recited above, examples of charged anionicsubstituents include anions of inorganic and organic acids, such assulfonate (—SO₃₁ ¹⁻), sulfinate, carboxylate, phosphinate, phosphonate,phosphate, and esters (such as alkyl esters) thereof. In someembodiments, the charged substituent is sulfonate. Examples of chargedcationic substituents include quaternary amines (—NR₃ ⁺), where R isindependently selected from C₁₋₆ alkyl, aryl, and arylalkyl. Othercharged cationic substituents include protonated primary, secondary, andtertiary amines, and well as guanidinium. In some embodiments, thecharged substituent is —N(CH₃)₃ ⁺.

In some embodiments, the ionic group consists solely of a chargedsubstituent. Examples of charged substituents include any of thosementioned above, such as sulfonate and —N(CH₃)₃ ⁺.

In some embodiments, the ionic group corresponds to a C₁₋₂₀ alkyl groupsubstituted with one or more charged substituents, wherein the C₁₋₂₀alkyl group is optionally further substituted with 1, 2, 3, 4, 5, or 6substituents independently selected from halo, cyano, nitro, and C₁₋₄haloalkyl, wherein 0, 1, 2, 3, 4, 5, or 6 carbon atoms of the alkylgroup are individually replaced with O, S, C(O), C(O)O, NR′, C(O)NR′,SO, SO₂, SO₂NR′, wherein R′ is H or C₁₋₆ alkyl, with the proviso thatthe replacement does not result in an unstable moiety (e.g., —O—O—,—O—S—, etc.).

Examples of ionic groups include a group selected from the followingformulae:

wherein y and z are independently selected from 0, 1, 2, 3, 4, 5, 6, 7,and 8. In some embodiments, y and z are independently selected from 1,2, 3, 4, 5, 6, 7, and 8. In some embodiments, y and z are independentlyselected from 1, 2, 3, and 4. In some embodiments, y and z are 0.

Further examples of ionic groups include a group selected from thefollowing formulae:

In some embodiments, the ionic group can contain two or more chargedsubstituents. For example, the ionic group can include both an anionicand a cationic substituent, forming a “zwitterionic group” (or“zwitterion”). Zwitterionic groups can be particularly useful assubstituents in the present invention because they incorporateadditional formal charges in the conjugate yet do not impact net totalcharge, thereby facilitating charge-balance. In some embodiments, azwitterionic group corresponds to a C₁₋₂₀ alkyl group substituted withat least one positively charged (cationic) substituent and at least onenegatively charged (anionic) group, such that the overall charge of thezwitterionic group is zero, and wherein the C₁₋₂₀ alkyl group isoptionally further substituted with 1, 2, 3, 4, 5, or 6 substituentsindependently selected from halo, cyano, nitro, and C₁₋₄ haloalkyl,wherein 0, 1, 2, 3, 4, 5, or 6 carbon atoms of the C₁₋₂₀ alkyl group areindividually replaced with O, S, C(O), C(O)O, NR′, C(O)NR′, SO, SO₂,SO₂NR′, wherein R′ is H or C₁₋₆ alkyl, with the proviso that thereplacement does not result in an unstable moiety (e.g., —O—O—, —O—S—,etc.).

In one embodiment, the zwitterionic group includes a sulfonate group anda quaternary amine of formula —NR₃ ⁺, wherein R is independentlyselected from C₁₋₆ alkyl, aryl, and arylalkyl. In one aspect, thezwitterionic group has the formula:

wherein w is 1, 2, 3, 4, 5, 6, 7, or 8. In some embodiments, thezwitterionic group has the formula:

II. Reduced Cyanine Dye Compounds

Compounds of Formula I-VII are useful as reactive oxygen species (ROS)probes for biochemical in vivo and in vitro applications. In thepresence of radicals (which may be present in inflamed tissues, tumortissues, during reaction of horseradish peroxidase (HRP) enzyme withH₂O₂, and the like), non-fluorescent hydrocyanines oxidize tofluorescent cyanine dyes. This property of hydrocyanine dyes can beexploited for the development of highly sensitive assay platforms or invitro and in vivo imaging probes. Tissues of interest, such as inflamedor tumor tissues, and processes of interest, such as the reaction ofhorseradish peroxidase (HRP) enzyme with H₂O₂, can produce higherconcentration of radical oxidants, which react with the hydrocyanine ordeuterocyanine compounds to produce fluorescent dyes.

Examples of ROS include, but are not limited to, oxygen, superoxide,peroxide, hydrogen peroxide, and hydroxyl radicals and ions. ROS areimplicated in a number of physiological processes, including redoxsignaling, pathogen response, aging, and certain transcriptionalprocesses. In tumor cells, for example, production of ROS as a result ofhypoxia has been shown to activate transcription factors that promotetumor growth.

Advantages of the compounds of the present invention include, e.g., veryhigh sensitivity, improved stability, and improved water solubility. Theapplications are novel and enable researchers to do experiments whichare not possible with the existing technologies. Quantitative detectionof ROS is also possible with a ratiometric probe (e.g., hydrocyanineattached with another always-on dye molecule a conjugate disclosedherein). The hydrocyanine dyes are used as a platform technology fordetecting ROS in biological samples in the entire gamut of the spectrumfrom visible to the NIR region.

A. Compounds of Formula I

In one aspect, the present invention provides a compound of Formula I:

Each R¹ is an independently selected alkyl group that is additionallysubstituted with from 0 to 1 R¹⁴ and from 0 to 1 -L-Y—Z; wherein thealkyl is optionally interrupted by at least one heteroatom or an ionicgroup.

In a preferred aspect, R¹ is not interrupted by a heteroatom.Alternatively, R¹ is interrupted by at least one ether, thioether,substituted amino, or amido group.

In a preferred aspect, R¹ is C₁-C₂₀ alkyl. In a more preferred aspect,R¹ is C₁-C₁₂ or C₂-C₈ alkyl. In a still more preferred aspect, R¹ is 2,3, or 4.

In another preferred aspect, R¹ is (CH₂)_(r)SO₃H or (CH₂)_(r)SO₃ ⁻; andr is an integer from 1 to 20. In a more preferred aspect, r is 2, 3, or4. Alternatively, R¹ is (CH₂)_(r)OH; and r is an integer from 2 to 6(e.g., 6-hydroxyhexyl).

In still another preferred aspect, R¹ is an alkyl group that isadditionally substituted with 1 R¹⁴. In a more preferred aspect, the R¹⁴is carboxy or sulfonato. In a still more preferred aspect, R¹⁴ issulfonato. Alternatively, R¹⁴ is hydroxy. In a yet still more preferredaspect, R¹⁴ is 3-sulfonatopropyl or 4-sulfonatobutyl.

In yet another preferred aspect, R¹ is an unbranched alkyl group that isadditionally substituted with 1 R¹⁴. In a more preferred aspect, R¹ isan unbranched alkyl group that is substituted with R¹⁴ at the end of thealkyl group opposite to its attachment point to the reduced cyanine dyeheterocyclic nitrogen. In a still more preferred aspect, R¹ is2-sulfonatoethyl, 3-sulfonatopropyl, 4-sulfonatobutyl, or5-sulfonatopentyl. In a yet still more preferred aspect, R¹ is3-sulfonatopropyl or 4-sulfonatobutyl; more preferably, R¹ is3-sulfonatopropyl.

R^(1a) is either hydrogen or deuterium. Alternatively, R^(1a) istritium.

Each R^(2a) and R^(2b) is a member independently selected from the groupconsisting of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl,amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, orsulfonatoalkyl; wherein a carbon of the member is additionallysubstituted with from 0 to 1 -L-Y—Z.

In a preferred aspect, all R^(2a) are the same substituent.Alternatively, all R^(2b) are the same substituent. More preferably, allR^(2a) are the same substituent, and all R^(2b) are the samesubstituent.

In another preferred aspect, R^(2a) and R^(2b) are the same. In a morepreferred aspect, R^(2a) and R^(2b) are alkyl, alkenyl, aminoalkyl,carboxyalkyl, or sulfonatoalkyl. In a still more preferred aspect,R^(2a) and R^(2b) are alkyl, carboxyalkyl, or sulfonatoalkyl. In a yetstill more preferred aspect, R^(2a) and R^(2b) are methyl.

In an alternative aspect, R^(2a) and R^(2b) are different. In a morepreferred aspect, R^(2a) is alkyl, and R^(2b) is selected from the groupof alkyl, alkenyl, aminoalkyl, carboxyalkyl, or sulfonatoalkyl. In astill more preferred aspect, R^(2a) is alkyl, and R^(2b) is selectedfrom the group of alkyl, carboxyalkyl, or sulfonatoalkyl. Yet still morepreferably, R^(2a) is methyl.

Each R³, R⁴, R⁵, and R⁶ is a member independently selected from thegroup consisting of hydrogen, alkyl, alkenyl, halo, hydroxyl, alkoxy,amino, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxyalkyl,carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl; wherein a carbonof the member is additionally substituted with from 0 to 1 -L-Y—Z.

In a first aspect, each R³, R⁴, R⁵, and R⁶ is a member independentlyselected from the group consisting of hydrogen, alkyl, alkenyl, halo,alkoxy, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxyalkyl,carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl. In a preferredaspect, each R³, R⁴, R⁵, and R⁶ is a member independently selected fromthe group of hydrogen, alkyl, carboxy, carboxyalkyl, sulfanato, andsulfanatoalkyl. In a more preferred embodiment, each R³, R⁴, R⁵, and R⁶is a member independently selected from the group of hydrogen andsulfanato.

In one aspect, at least one pair of R³, R⁴, R⁵, or R⁶ is the same (i.e.,the R^(n) substituent is not independently selected, but is the same asthe other R^(n) substituent). This aspect can be combined with otheraspects specifying the number or type of dye substituents (e.g., exactlytwo members of the groups R³, R⁴, R⁵, and R⁶ are hydrogen, and the twomembers are the pair of R⁴s). Alternatively, at least two, at leastthree, or all four pairs of R³, R⁴, R⁵, or R⁶ are the same. Morepreferably, the dye is symmetric or pseudo-symmetric (i.e., R¹, R^(2a),and R^(2b) are also not independently selected, but are the same as theother R¹, R^(2a), and R^(2b) substituents).

In an alternative aspect, at least one member of the groups R³, R⁴, R⁵,and R⁶ is hydrogen. Alternatively, exactly one member of the groups R³,R⁴, R⁵, and R⁶ is hydrogen. In a preferred aspect, at least one pair ofsubstituents selected from the pairs R³ and R⁴; R³ and R⁵; R³ and R⁶; R⁴and R⁵; R⁴ and R⁶; and R⁵ and R⁶ is hydrogen. Alternatively, exactlytwo, exactly three, exactly four, exactly five, or exactly six membersof the groups R³, R⁴, R⁵, and R⁶ are hydrogen. In another aspect,exactly four members of the groups R³, R⁴, R⁵, and R⁶ are hydrogen.Alternatively, exactly five members of the groups R³, R⁴, R⁵, and R⁶ arehydrogen. In a still more preferred aspect, R³, R⁴, and R⁶ are hydrogen.

In another alternative aspect, at least one member of the groups R³, R⁴,R⁵, and R⁶ is sulfonato or sulfonatoalkyl. Alternatively, exactly onesubstituent selected from the groups R³, R⁴, R⁵, and R⁶ is sulfonato orsulfonatoalkyl. In a preferred aspect, R⁵ is sulfonato. In still anotheraspect, both members of a pair of substituents selected from the pairsR³ and R⁴; R³ and R⁵; R³ and R⁶; R⁴ and R⁵; R⁴ and R⁶; and R⁵ and R⁶ areeach a member independently selected from the group of sulfonato orsulfonatoalkyl. Alternatively, exactly two, exactly three, exactly four,exactly five, or exactly six members of the groups R³, R⁴, R⁵, and R⁶are each a member independently selected from the group of sulfonato orsulfonatoalkyl.

In another alternative aspect, at least one member of the group R³, R⁴,R⁵, and R⁶ is anionic at physiological pH (e.g., sulfonato —SO₃ ⁻,carboxy —CO₂ ⁻). Alternatively, exactly one member of the group R³, R⁴,R⁵, and R⁶ is anionic at physiological pH. In a preferred aspect, R⁵ isanionic at physiological pH. In still another aspect, each member of apair of substituents selected from the pairs R³ and R⁴; R³ and R⁵; R³and R⁶; R⁴ and R⁵; R⁴ and R⁶; and R⁵ and R⁶ is anionic at physiologicalpH. Alternatively, exactly two, exactly three, exactly four, exactlyfive, or exactly six members of the groups R³, R⁴, R⁵, and R⁶ areanionic at physiological pH. Alternatively, exactly two, exactly three,or exactly four members of the groups R³, R⁴, R⁵, and R⁶ are anionic atphysiological pH.

In another alternative aspect, at least one member of the groups R³, R⁴,R⁵, and R⁶ is halo. Alternatively, exactly one substituent selected fromthe groups R³, R⁴, R⁵, and R⁶ is halo. Alternatively, exactly two,exactly three, or exactly four members of the groups R³, R⁴, R⁵, and R⁶are halo.

R⁸, R⁹, R¹⁰, R¹¹ and R¹² are each a member independently selected fromthe group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy,sulfonato, hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido,thioacetyl, and -L-Y—Z. In one preferred embodiment, at least one memberselected from the group consisting of R⁸, R⁹, and R¹⁰ is halo. Morepreferably, at least one member selected from the group consisting ofR⁸, R⁹, and R¹⁰ is fluoro or chloro.

In one aspect, R⁸ is halo; more preferably, fluoro or chloro.Preferably, R⁹, R¹⁰, R¹¹, and R¹² are each a member independentlyselected from the group consisting of hydrogen, alkyl, alkoxy, halo,sulfonato, and -L-Y—Z.

In a second aspect, R⁸ is hydrogen, alkyl, alkoxy, or halo. Morepreferably, R⁸ is fluoro; alternatively, R⁸ is chloro.

In an alternative preferred aspect, R⁸ is hydrogen.

Alternatively, R⁸ is a carboxyalkyl. Preferably, R⁸ is a lower alkylgroup with a carboxy-substituent. More preferably, R⁸ is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, R⁸ is 5-carboxypentyl or2-carboxyethyl. In some aspects, the carboxyalkyl is optionallyinterrupted by at least one heteroatom (e.g., 4-carboxybutoxy;2-((2-carboxy)ethyloxy)ethyl).

Alternatively, R⁸ is carboxyl, alkoxycarbonyl, or amido; morepreferably, R⁸ is carboxyl. Alternatively, R⁸ is -L-Y—Z.

In one aspect, R¹⁰ is halo; more preferably, fluoro or chloro.Preferably, R⁸, R⁹, R¹¹, and R¹² are each a member independentlyselected from the group consisting of hydrogen, alkyl, alkoxy, halo,sulfonato, and -L-Y—Z.

In a second aspect, R¹⁰ is hydrogen, alkyl, alkoxy, or halo. In anothermore preferred aspect, R¹⁰ is fluoro; alternatively, R¹⁰ is chloro.

In an alternative preferred aspect, R¹⁰ is hydrogen.

Alternatively, R¹⁰ is a carboxyalkyl. Preferably, R¹⁰ is a lower alkylgroup with a carboxy-substituent. More preferably, R¹⁰ is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, R¹⁰ is 5-carboxypentyl or2-carboxyethyl. In some aspects, the carboxyalkyl is optionallyinterrupted by at least one heteroatom (e.g., 4-carboxybutoxy;2-((2-carboxy)ethyloxy)ethyl).

Alternatively, R¹⁰ is carboxyl, alkoxycarbonyl, or amido; morepreferably, R¹⁰ is carboxyl. Alternatively, R¹⁰ is -L-Y—Z.

In one aspect, R⁹ is -L-Y—Z. Preferably, R⁸, R¹⁰, R¹¹, and R¹² are eacha member independently selected from the group consisting of hydrogen,alkyl, alkoxy, halo, sulfonato, and -L-Y—Z.

In a second aspect, R⁹ is hydrogen, alkyl, alkoxy, or halo. In anothermore preferred aspect, R⁹ is fluoro; alternatively, R⁹ is chloro.

In an alternative preferred aspect, R⁹ is hydrogen.

Alternatively, R⁹ is a carboxyalkyl. Preferably, R⁹ is a lower alkylgroup with a carboxy-substituent. More preferably, R⁹ is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, R¹⁰ is 5-carboxypentyl or2-carboxyethyl. In some aspects, the carboxyalkyl is optionallyinterrupted by at least one heteroatom (e.g., 4-carboxybutoxy;2-((2-carboxy)ethyloxy)ethyl).

Alternatively, R⁹ is carboxyl, alkoxycarbonyl, or amido; morepreferably, R⁹ is carboxyl.

In one aspect, R¹¹ and R¹² are each a member independently selected fromthe group of hydrogen, alkyl, alkenyl, halo, alkoxy, sulfonato,hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido, thioacetyl, and-L-Y—Z. Preferably, R¹¹ and R¹² are each a member independently selectedfrom the group of hydrogen, alkyl, halo, and sulfonato. More preferably,R¹¹ and R¹² are each a member independently selected from the group ofhydrogen, halo, and sulfonato.

In a second aspect, R¹¹ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹¹ is halo; preferably, R¹¹ is fluoro or chloro. Inan alternative aspect, R¹¹ is hydrogen. Alternatively, R¹⁰ and R¹¹ arehydrogen.

In a third aspect, R¹² is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹² is halo; preferably, R¹² is fluoro or chloro. In astill more preferred aspect, R¹⁰ and R¹² are halogen, preferably fluoroor chloro. Alternatively, R¹¹ and R¹² are halogen, preferably fluoro orchloro. In a yet still more preferred aspect, R¹⁰, R¹¹, and R¹² arehalogen, preferably fluoro or chloro.

In a fourth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3-substituted with independently selected substituentsother than hydrogen, wherein the 1-substituent is the polymethine bridge(e.g., R⁸ and R⁹ are the same halo group; R⁸ and R⁹ are different halogroups; R⁸ is halo- and R⁹ is -L-Y—Z). Alternatively, the ring is1,2,4-substituted. Alternatively, the ring is 1,2,5-substituted.Alternatively, the ring is 1,2,6-substituted. Alternatively, the ring is1,3,4-substituted. Alternatively, the ring is 1,3,5-substituted.Alternatively, the ring is 1,3,6-substituted. Preferably, at least twoof the substituents are halo; more preferably, fluoro or chloro.

In a fifth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3,4-substituted with independently selected substituentsother than hydrogen, wherein the 1-substituent is the polymethinebridge. Alternatively, the ring is 1,2,3,5-substituted. Alternatively,the ring is 1,2,3,6-substituted. Alternatively, the ring is1,2,4,5-substituted. Alternatively, the ring is 1,2,4,6-substituted.Alternatively, the ring is 1,2,5,6-substituted. Alternatively, the ringis 1,3,4,5-substituted. Alternatively, the ring is 1,3,4,6-substituted.Alternatively, the ring is 1,3,5,6-substituted. Preferably, at least twoof the substituents are halo; more preferably, fluoro or chloro.Alternatively and preferably, at least three of the substituents arehalo; more preferably, fluoro or chloro.

In a sixth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3,4,5-substituted with independently selectedsubstituents other than hydrogen, wherein the 1-substituent is thepolymethine bridge. Alternatively, the ring is 1,3,4,5,6-substituted.Alternatively, the ring is 1,2,4,5,6-substituted. Alternatively, thering is 1,2,3,5,6-substituted. Alternatively, the ring is1,2,3,4,6-substituted. Alternatively, the ring is independentlysubstituted at each ring position.

Preferably, at least two of the phenyl ring substituents are halo; morepreferably. fluoro or chloro. Alternatively, at least three of thesubstituents are halo; more preferably. fluoro or chloro (e.g., R⁸, R¹⁰,and R¹² are halo). Alternatively, at least four of the substituents arehalo; more preferably. fluoro or chloro (e.g., R⁸, R⁹, R¹¹, and R¹² arehalo).

In a seventh aspect, R⁸, R⁹, R¹⁰, R¹¹, and R¹² are each a memberindependently selected from the group of hydrogen, alkyl, alkoxy, halo,sulfonato, and sulfonatoalkyl.

Fluoro substitution has been shown to increase quantum yield andphotostability in fluorescein dyes as well as lowering dye pK_(a). SeeSun, W.-C. et al. J. Org. Chem. 1997, 62, 6469-6475. In an eighthaspect, at least one member of the group R⁸, R⁹, R¹⁰, R¹¹, and R¹² is afluoro substituent. Alternatively, at least one member of the groups R³,R³, R⁴, R⁵, R⁶, and R¹⁴ is a fluoro substituent. In yet another aspect,at least two members of the groups R³, R⁴, R, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹²,and R¹⁴ are fluoro substituents. In yet another aspect, at least threemembers of R³, R⁴, R, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ are fluorosubstituents. In yet another aspect, at least four or at least fivemembers of the groups R³, R⁴, R, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ arefluoro substituents.

As demonstrated in the examples, chloro substitution also has afavorable effect on the dye properties, much as the fluoro group does.In a ninth aspect, at least one member of the group R⁸, R⁹, R¹⁰, R¹¹,and R¹² is a chloro substituent. Alternatively, at least one member ofthe groups R³, R⁴, R, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ is a chlorosubstituent. In yet another aspect, at least two members of the groupsR³, R⁴, R, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ are chloro substituents.In yet another aspect, at least three members of the groups R³, R⁴, R,R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ are chloro substituents. In yetanother aspect, at least four or at least five members of the groups R³,R⁴, R, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ are chloro substituents.

Each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, and alkoxycarbonyl. In a preferred embodiment, R¹³ iscarboxyl or alkoxycarbonyl. In a more preferred embodiment, R¹³ iscarboxyl. Alternatively, R¹³ is cyano. Alternatively, R¹³ is hydroxyl.

Each R¹⁴ is a member independently selected from the group consisting ofalkyl, alkenyl, halo, hydroxyl, alkoxy, amino, amido, amidoalkyl, cyano,cyanoalkyl, carboxyl, alkoxycarbonyl, amido, sulfonato, sulfonatoalkyl,thioacetyl, thioacetylalkyl, alkoxycarbonylalkyl, and alkoxyalkyl;wherein the alkyl or alkenyl is additionally substituted with from 0 to1 R¹³ and from 0 to 1 -L-Y—Z. In a preferred aspect, R¹⁴ is alkyl,alkenyl, carboxyl, alkoxycarbonyl, amido, alkoxycarbonylalkyl, halo,sulfonato, or sulfonatoalkyl. Alternatively, R¹⁴ is carboxyalkyl,hydroxyalkyl, halo, sulfonato, or sulfonatoalkyl. In an alternativeaspect, R¹⁴ is alkyl or alkyl substituted with 1 R¹³. Alternatively, R¹⁴is halo or sulfonato. Alternatively, R¹⁴ is sulfonato. Alternatively,R¹⁴ is hydroxy.

In an alternative aspect, at least one R¹⁴ substituent is zwitterionicat physiological pH (e.g., an alkyl group with anionic sulfonato —SO₃ ⁻and a cationic trialkylammonium group substituents). Alternatively,exactly one R¹⁴ substituent is zwitterionic at physiological pH. Instill another aspect, at least one pair of R¹⁴ substituents iszwitterionic at physiological pH. Alternatively, exactly one, exactlytwo, exactly three, or exactly four R¹⁴ substituents are zwitterionic atphysiological pH.

Each L is an optional member independently selected from the groupconsisting of a bond, a C₁-C₂₀ alkylene, and a C₁-C₂₀ alkenylene;wherein the alkylene or alkenylene is optionally interrupted by at leastone heteroatom. In a preferred aspect, L is a bond, with the provisothat L is not a bond when that would produce a highly unstable structure(e.g., N-L-R¹³, if R¹³ is —CO₂H). Alternatively, L is a C₁-C₁₄ alkylene;more preferably, L is a C₁-C₁₀ alkylene or a C₁-C₆ alkylene.Alternatively, L is a C₁-C₁₂ alkylene interrupted by ether linkages(e.g., a polyethylene glycol oligomer).

In a preferred aspect, the alkylene or alkenylene is not interrupted bya heteroatom. Alternatively, L is interrupted by at least one ether,thioether, substituted amino, or amido group.

Each Y is an optional member independently selected from the groupconsisting of a bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—,—NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—, —NZC(O)—, and —C(O)NZ—. In a preferredaspect, Y is a bond. Alternatively, Y is —O—. Alternatively, Y is anamido group optionally substituted with R¹⁵ at the amido nitrogen.

Each Z is independently selected from the group consisting of R¹³ andR¹⁶. Alternatively, each Z is an R¹⁴ substituent, wherein the R¹⁴substituent is not substituted with any -L-Y—Z group. In a morepreferred aspect, Z is C₁-C₆ alkyl. Alternatively, Z is interrupted byether linkages (e.g., a polyethylene glycol oligomer). In a still morepreferred aspect, Z is carboxyalkyl or alkyl with an activated acylsubstituent. In a yet still more preferred aspect, Z is 5-carboxypentylor 4-carboxybutyl.

In an alternative preferred aspect, Z is a carboxyalkyl. Preferably, Zis a lower alkyl group with a carboxy-substituent. More preferably, Z is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, Z is 5-carboxypentyl or2-carboxyethyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R¹³; R¹³ is carboxyl or activated acyl; and t is an integerfrom 0 to 10, such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.Alternatively, t is an integer from 1 to 10.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R¹³ or R¹⁶ that is directly bonded to thephenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastthree carbons. Alternatively, Z has at least three carbons.

In yet still another alternative preferred aspect, -L-Y—Z has at leastfour carbons. Alternatively, Z has at least four carbons.

In an alternative embodiment, —Y—Z is a member selected from the groupconsisting of —N(Z)₂, —N(Z)C(O)Z, and —C(O)N(Z)₂, and the two Z groupsmay optionally be linked to form a cycloalkynyl group.

In one embodiment, each R¹⁵ is a member independently selected from thegroup consisting of alkyl and alkoxycarbonylalkyl; wherein the alkyl isoptionally interrupted by at least one heteroatom or an ionic group(e.g., a charged alkylammonium group, such as that in—CH₂(NMe₂)CH₂CH₂CH₂—). Preferably, each R¹⁵ is an independently selectedalkyl.

In an alternative embodiment, R¹⁵ is a member selected from the group ofalkyl and alkoxycarbonylalkyl; wherein the alkyl is optionallyinterrupted by at least one heteroatom or an ionic group (e.g., acharged alkylammonium group, such as that in —CH₂(NMe₂)CH₂CH₂CH₂—). In apreferred aspect, R¹⁵ is alkyl. In a more preferred aspect, R¹⁵ is loweralkyl. In another aspect, R¹⁵ is interrupted by ether linkages (e.g., apolyethylene glycol oligomer).

In one embodiment, each R¹⁶ is independently a member selected from thegroup of activated acyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl,isothiocyanato, iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl,and vinyl sulfonyl. In a preferred aspect, R¹⁶ is activated acyl,maleimidyl, phosphoramidityl, or glycidyl. In a more preferredembodiment, R¹⁶ is activated acyl. Alternatively, R¹⁶ is activatedester. In a still more preferred embodiment, R¹⁶ issuccinimidyloxy-ester or sulfosuccinimidyloxy-ester.

In an alternative embodiment, each R¹⁶ is independently a memberselected from the group consisting of activated acyl, acrylamido,optionally substituted alkylsulfonate ester, azido, optionallysubstituted arylsulfonate ester, optionally substituted amino,aziridino, boronato, cycloalkynyl, cycloalkynylcarbonyl, diazo, formyl,glycidyl, halo, haloacetamidyl, haloalkyl, haloplatinato, halotriazino,hydrazinyl, imido ester, isocyanato, isothiocyanato, maleimidyl,mercapto, phosphoramidityl, a photoactivatable moiety, vinyl sulfonyl,alkynyl, cycloalkynyl, spirocycloalkynyl, a pegylated azido, a pegylatedalkynyl, a pegylated cycloalkynyl, a pegylated spirocycloalkynyl, ano-diarylphosphino aryl ester, and an ortho substituted phosphine oxidearyl ester. Preferably, “optionally substituted amino” is selected fromthe group consisting of —NH₂, —NHR₁₅, and —N(R₁₅)₂. Alternatively, eachR¹⁶ is independently a member selected from the group consisting ofactivated acyl, azido, amino, alkylamino, diazo, hydrazinyl, imidoester, isocyanato, isothiocyanato, maleimidyl, phosphoramidityl,alkynyl, cycloalkynyl, cycloalkynylcarbonyl, spirocycloalkynyl, apegylated azido, a pegylated alkynyl, a pegylated cycloalkynyl, and apegylated spirocycloalkynyl. Alternatively, each R¹⁶ is independently amember selected from the group consisting of activated acyl, amino,alkylamino, imido ester, isothiocyanato, and maleimidyl. Alternatively,each R¹⁶ is independently a member selected from the group consisting ofazido, alkynyl, cycloalkynyl, cycloalkynylcarbonyl, spirocycloalkynyl, apegylated azido, a pegylated alkynyl, a pegylated cycloalkynyl, and apegylated spirocycloalkynyl.

In a preferred embodiment, the compounds of Formula I have thestructures:

In one embodiment, the parent compound's oxidized form has a balancedcharge. In a preferred aspect, the compound's net anionic charge in theoxidized state is balanced by alkali metal counterions (e.g., sodium orpotassium). In a preferred aspect, in the parent compound's oxidizedstate, at least one of the counterions is sodium. Alternatively, all ofthe counterions are sodium.

In one embodiment, the compound's net cationic charge in the oxidizedstate is balanced by organic anions (e.g., acetate, chloride, sulfonate,or formate). In a preferred aspect, in the parent compound's oxidizedstate, at least one of the counterions is chloride or acetate.Alternatively, all of the counterions are chloride or acetate.

The compound may also incorporate covalent bonds to both cationic andanionic groups to produce a balanced charge. Embodiments of suchcompounds are set forth in U.S. Patent Publication No. 2012/0028291,which is incorporated by reference. In a preferred aspect, thecompound's charge in the oxidized state is balanced by a combination ofalkali metal counterions (e.g., sodium or potassium) andtetraalkylammonium substituents (e.g., a trimethylammonium substituent;a triethylammonium substituent; or a methyl diethylammoniumsubstituent).

B. Compounds of Formula II

In another embodiment, the present invention provides a compound ofFormula II:

R¹ and R^(1a) are independently selected from L-Y—Z and an alkyl groupthat is additionally substituted with from 0 to 1 R¹³; wherein the alkylis optionally interrupted by at least one heteroatom or an ionic group(e.g., a charged alkylammonium group, such as that in—CH₂(NMe₂)CH₂CH₂CH₂—). In a preferred aspect, R¹ and R^(1a) areindependently a C₂-C₁₂ alkyl. In a more preferred aspect, R¹ and R^(1a)are independently C₂-C₈ alkyl. In a still more preferred aspect, R¹ andR^(1a) are independently C₂-C₆ alkyl. In a yet still more preferredaspect, R¹ and R^(1a) are independently ethyl, propyl, butyl, or pentyl,and R¹ is additionally substituted with 1 R¹³. In one aspect, this R¹³substituent is sulfonato; alternatively, R¹³ is hydroxyl.

In a preferred aspect, R¹ and R^(1a) are independently (CH₂)_(r)SO₃H or(CH₂)_(r)SO₃ ⁻; and r is an integer from 1 to 20. In a more preferredaspect, r is 2, 3, or 4. Alternatively, R¹ is (CH₂)_(r)OH; and r is aninteger from 2 to 6 (e.g., 6-hydroxyhexyl).

In one aspect, R¹ and R^(1a) are independently an alkyl group that isadditionally substituted with 1 R¹³, wherein R¹³ is selected from thegroup of hydroxyl, amino, carboxy, and sulfonato. In a more preferredaspect, the R¹³ substituent of R¹ and R^(1a) are independently a carboxyor sulfonato. In a still more preferred aspect, the R¹³ substituent ofR¹ or R^(1a) is sulfonato. In a yet still more preferred aspect, R¹ andR^(1a) are independently a sulfonatoethyl, sulfonatopropyl,sulfonatobutyl, or sulfonatopentyl.

In another alternative preferred aspect, R¹ and R^(1a) are independentlyan unbranched alkyl group that is additionally substituted with 1 R¹³.In a more preferred aspect, R¹ is an unbranched alkyl group that issubstituted with R¹³ at the end of the alkyl group opposite to itsattachment point to the reduced cyanine dye heterocyclic nitrogen. In astill more preferred aspect, R¹ is 2-sulfonatoethyl, 3-sulfonatopropyl,4-sulfonatobutyl, or 5-sulfonatopentyl. In a yet still more preferredaspect, R¹ is 3-sulfonatopropyl or 4-sulfonatobutyl.

R^(1a′) and R^(1′) are independently either hydrogen or deuterium.Alternatively, R^(1a) or R^(1′) is tritium.

Each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl. In apreferred embodiment, R¹³ is carboxyl, amido, or alkoxycarbonyl. In amore preferred embodiment, R¹³ is carboxyl. Alternatively, R¹³ issulfonato.

Each R¹⁴ is a member independently selected from the group of alkyl,alkenyl, halo, hydrogen, hydroxyl, alkoxy, amino, cyano, carboxyl,alkoxycarbonyl, amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl;wherein the R¹⁴ alkyl is additionally substituted with from 0 to 1 R¹³;and wherein at least one R¹⁴ is sulfonato. Alternatively, each R¹⁴ is amember independently selected from the group of alkyl, alkenyl, halo,hydrogen, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl; wherein the R¹⁴alkyl is additionally substituted with from 0 to 2 R¹³.

In a preferred aspect, at least one R¹⁴ is alkyl, alkenyl, carboxyl,alkoxycarbonyl, amido, or alkoxycarbonylalkyl. Alternatively, at leasttwo R¹⁴ are sulfonato. Alternatively, at least one R¹⁴ is hydroxy. In amore preferred aspect, at least one R¹⁴ is alkyl or alkyl substitutedwith 1 R¹³. Alternatively, at least one R¹⁴ is carboxyalkyl,hydroxyalkyl, or sulfonatoalkyl. In some aspects, the carboxyalkyl,hydroxyalkyl, or sulfonatoalkyl is optionally interrupted by at leastone heteroatom (e.g., 4-carboxybutoxy; 2-(hydroxyethyloxy)ethyl).

In one aspect, at least two of the R¹⁴ substituents are eachindependently carboxy, carboxyalkyl, sulfonato, or sulfonatoalkyl. In astill more preferred aspect, at least two of the R¹⁴ substituents areeach independently sulfonato or sulfonatoalkyl. In a yet more preferredaspect, each of the R¹⁴ substituents is sulfonato.

In one aspect, at least one pair of the R¹⁴ substituents is the same(i.e., the R^(n) substituent is not independently selected, but is thesame as the other R^(n) substituent). Alternatively, at least two pairsof the R¹⁴ substituents are the same. More preferably, the dye issymmetric or pseudo-symmetric (i.e., the R¹⁴ substituents on the dyeindoline rings are also not independently selected, but each R¹⁴substituent is the same as the analogous R¹⁴ substituents on the otherring).

In an alternative aspect, at least one R¹⁴ substituent is hydrogen.Alternatively, exactly R¹⁴ substituent is hydrogen. In a preferredaspect, at least one pair of R¹⁴ substituents is hydrogen.Alternatively, exactly two, exactly three, or exactly four R¹⁴substituents are hydrogen. In another aspect, exactly four R¹⁴substituents are hydrogen.

In another alternative aspect, at least one R¹⁴ substituent is sulfonatoor sulfonatoalkyl. Alternatively, exactly one R¹⁴ substituent issulfonato or sulfonatoalkyl. In still another aspect, at least one pairof R¹⁴ substituents is each a member independently selected from thegroup of sulfonato or sulfonatoalkyl. Alternatively, exactly one,exactly two, exactly three, or exactly four R¹⁴ substituents are each amember independently selected from the group of sulfonato orsulfonatoalkyl.

In another alternative aspect, at least one R¹⁴ substituent is anionicat physiological pH (e.g., sulfonato —SO₃ ⁻, carboxy —CO₂ ⁻).Alternatively, exactly one R¹⁴ substituent is anionic at physiologicalpH. In still another aspect, at least one pair of R¹⁴ substituents isanionic at physiological pH. Alternatively, exactly one, exactly two,exactly three, or exactly four R¹⁴ substituents are anionic atphysiological pH.

In another alternative aspect, at least one R¹⁴ substituent iszwitterionic at physiological pH (e.g., an alkyl group with anionicsulfonato —SO₃ ⁻ and a cationic trialkylammonium group substituents).Alternatively, exactly one R¹⁴ substituent is zwitterionic atphysiological pH. In still another aspect, at least one pair of R¹⁴substituents is zwitterionic at physiological pH. Alternatively, exactlyone, exactly two, exactly three, or exactly four R¹⁴ substituents arezwitterionic at physiological pH.

In another alternative aspect, at least one R¹⁴ substituent is halo.Alternatively, exactly one R¹⁴ substituent is halo. Alternatively,exactly two, exactly three, or exactly four R¹⁴ substituents are halo.

L is an optional member selected from the group of a bond, a C₁-C₁₀alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene or alkenylene isoptionally interrupted by at least one heteroatom. In a preferredaspect, L is not present. Alternatively, L is a C₁-C₁₀ alkyleneinterrupted by one or more ether linkages (e.g., a polyethylene glycololigomer).

Y is an optional member selected from the group of a bond, —O—, —S—,—NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—,—NZC(O)—, and —C(O)NZ—. In a preferred aspect, Y is a bond.Alternatively, Y is —O—. Alternatively, Y is an amido group optionallysubstituted with R¹⁵ at the amido nitrogen.

Each Z is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ and R¹⁶; wherein thealkyl is optionally interrupted by at least one heteroatom. In a morepreferred aspect, Z is C₁-C₆ alkyl. Alternatively, Z is interrupted byether linkages (e.g., a polyethylene glycol oligomer). In a still morepreferred aspect, Z is carboxyalkyl or sulfonatoalkyl. In a yet stillmore preferred aspect, Z is 5-carboxypentyl or 4-carboxybutyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R¹³; R¹³ is carboxyl or activated acyl; and t is an integerfrom 1 to 10, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. Alternatively, tis an integer from 0 to 10.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R¹³ or R¹⁶ that is directly bonded to thephenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastfour carbons. Alternatively, Z has at least four carbons.

R¹⁵ is a member selected from the group of alkyl andalkoxycarbonylalkyl; wherein the alkyl is optionally interrupted by atleast one heteroatom. In a preferred aspect, R¹⁵ is alkyl. In a morepreferred aspect, R¹⁵ is lower alkyl. Alternatively, R¹⁵ is interruptedby ether linkages (e.g., a polyethylene glycol oligomer).

Each R¹⁶ is independently a member selected from the group of activatedacyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl, isothiocyanato,iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl, and vinylsulfonyl. In a preferred aspect, R¹⁶ is activated acyl, maleimidyl,phosphoramidityl, or glycidyl. In a more preferred embodiment, R¹⁶ isactivated acyl. Alternatively, R¹⁶ is activated ester. In a still morepreferred embodiment, R¹⁶ is succinimidyloxy-ester orsulfosuccinimidyloxy-ester.

In certain instances, the compounds of Formula II have the formula:

wherein R^(1′) and R^(1a′) are each independently hydrogen or deuterium,M is an alkali metal cation, and R² is CO₂H or CO₂M. Preferably, M isNa⁺.

In the oxidized state, the parent compound has a balanced charge. In apreferred aspect, the compound's net anionic charge in the oxidizedstate is balanced by alkali metal counterions (e.g., sodium orpotassium). In a preferred aspect, in the oxidized state, at least oneof the counterions is sodium. Alternatively, all of the counterions aresodium.

In one embodiment, the compound's net cationic charge in the oxidizedstate is balanced by organic anions (e.g., acetate, chloride, sulfonate,orformate). In a preferred aspect, in the oxidized state, at least oneof the counterions is chloride or acetate. Alternatively, all of thecounterions are chloride or acetate.

The compound may also incorporate covalent bonds to both cationic andanionic groups to produce a balanced charge. Embodiments of suchcompounds are set forth in U.S. Patent Publication No. 2012/0028291,which is incorporated by reference. In a preferred aspect, thecompound's charge in the oxidized state is balanced by a combination ofalkali metal counterions (e.g., sodium or potassium) andtetraalkylammonium substituents (e.g., a trimethylammonium substituent;a triethylammonium substituent; or a methyl diethylammoniumsubstituent).

C. Compounds of Formula III

In one embodiment, the present invention provides a compound of FormulaIII:

R¹ is independently an alkyl group that is additionally substituted withfrom 0 to 1 R¹³; wherein the alkyl group is optionally interrupted by atleast one heteroatom (e.g., an ethyl, such as in a poly(ethyleneglycol)) or an ionic group (e.g., a charged alkylammonium group, such asthat in —CH₂(NMe₂)CH₂CH₂CH₂—). In a preferred aspect, R¹ is C₂-C₁₂alkyl. In a alternative aspect, R¹ is C₁-C₆ alkyl (e.g., methyl). In amore preferred aspect, R¹ is C₂-C₈ alkyl. In a still more preferredaspect, R¹ is C₂-C₆ alkyl. In a yet still more preferred aspect, R¹ isethyl, propyl, butyl, pentyl, or hexyl, and R¹ is additionallysubstituted with 1 R¹³ (e.g., 3-sulfonylpropyl; 6-hydroxyhexyl).

In a preferred aspect, R¹ is (CH₂)_(r)SO₃H or (CH₂)_(r)SO₃ ⁻; and r isan integer from 1 to 20. In a more preferred aspect, r is 2, 3, or 4.Alternatively, R¹ is (CH₂)_(r)OH; and r is an integer from 2 to 6 (e.g.,6-hydroxyhexyl).

In one aspect, R¹ is an alkyl group that is additionally substitutedwith 1 R¹³ wherein R¹³ is selected from the group of hydroxyl, amino,carboxy, and sulfonato. In a more preferred aspect, the R¹³ substituentof R¹ is carboxy or sulfonato. In a still more preferred aspect, the R¹³substituent of R¹ is sulfonato. In a yet still more preferred aspect, R¹is sulfonatoethyl, sulfonatopropyl, sulfonatobutyl, or sulfonatopentyl.

In another alternative preferred aspect, R¹ is an unbranched alkyl groupthat is additionally substituted with 1 R¹³. In a more preferred aspect,R¹ is an unbranched alkyl group that is substituted with R¹³ at the endof the alkyl group opposite to its attachment point to the reducedcyanine dye heterocyclic nitrogen. In a still more preferred aspect, R¹is 2-sulfonatoethyl, 3-sulfonatopropyl, 4-sulfonatobutyl, or5-sulfonatopentyl. In a yet still more preferred aspect, R¹ is3-sulfonatopropyl or 4-sulfonatobutyl.

R^(1a) is either hydrogen or deuterium. Alternatively, R^(1a′) istritium.

R^(2a) and R^(2b) are each a member independently selected from thegroup of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl,amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, orsulfonatoalkyl.

In a preferred aspect, R^(2a) and R^(2b) are the same. In a morepreferred aspect, R^(2a) and R^(2b) are alkyl, alkenyl, aminoalkyl,carboxyalkyl, or sulfonatoalkyl. In a still more preferred aspect,R^(2a) and R^(2b) are alkyl, carboxyalkyl, or sulfonatoalkyl. In a yetstill more preferred aspect, R^(2a) and R^(2b) are methyl.

In an alternative preferred aspect, R^(2a) and R^(2b) are different. Ina more preferred aspect, R^(2a) is alkyl, and R^(2b) is selected fromthe group of alkyl, alkenyl, aminoalkyl, carboxyalkyl, orsulfonatoalkyl. In a still more preferred aspect, R^(2a) is alkyl, andR^(2b) is selected from the group of alkyl, carboxyalkyl, orsulfonatoalkyl.

R³ and R⁴ are each a member independently selected from the group ofhydrogen, alkyl, alkenyl, halo, hydroxyl, alkoxy, cyano, carboxyl,alkoxycarbonyl, amido, amino, sulfonato, alkoxyalkyl, carboxyalkyl,alkoxycarbonylalkyl, and sulfonatoalkyl.

In a first aspect, R³ and R⁴ are each a member independently selectedfrom the group of hydrogen, alkyl, alkenyl, halo, alkoxy, cyano,carboxyl, alkoxycarbonyl, amido, amino, sulfonato, alkoxyalkyl,carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl. In a preferredaspect, R³ and R⁴ are each a member independently selected from thegroup of hydrogen, alkyl, carboxy, carboxyalkyl, sulfanato, andsulfanatoalkyl. In a more preferred embodiment, R³, and R⁴ are each amember independently selected from the group of hydrogen and sulfanato.

In another alternative aspect, at least one member of the group R³ andR⁴ is sulfonato or sulfonatoalkyl. Alternatively, exactly onesubstituent selected from the group R³ and R⁴ is sulfonato orsulfonatoalkyl. In a preferred aspect, R³ is sulfonato. In still anotheraspect, R³ and R⁴ is selected independently from the group of sulfonatoor sulfonatoalkyl. Alternatively, exactly two members of the group R³and R⁴ are sulfonato or sulfonatoalkyl.

In another alternative aspect, at least one member of the group R³ andR⁴ is anionic at physiological pH (e.g., sulfonato —SO₃ ⁻, carboxy —CO₂⁻). Alternatively, exactly two members of the group R³ and R⁴ areanionic at physiological pH.

R⁸ and R⁹ are each a member independently selected from the group ofhydrogen, alkyl, alkenyl, halo, alkoxy, sulfonato, and -L-Y—Z; whereinexactly one member selected from the group of R⁸ and R⁹ is -L-Y—Z.

In one aspect, R⁸ is -L-Y—Z. Alternatively, R⁹ is -L-Y—Z.

In a second aspect, R⁸ is hydrogen, alkyl, alkoxy, or halo. In apreferred aspect, R⁸ is hydrogen. In another preferred aspect, R⁸ isfluoro.

Alternatively, R⁹ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R⁹ is 5-carboxypentyl. Alternatively, R⁹ is4-carboxybutyl.

R¹⁰, R¹¹, and R¹² are each a member independently selected from thegroup of hydrogen, alkyl, alkenyl, halo, alkoxy, and sulfonato.

In a first aspect, R¹⁰ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹⁰ is hydrogen. Alternatively, R¹⁰ is fluoro.

In a second aspect, R¹¹ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹¹ is hydrogen. Alternatively, R¹¹ is fluoro. In astill more preferred aspect, R¹⁰ and R¹¹ are hydrogen.

In a third aspect, R¹² is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹² is hydrogen. Alternatively, R¹² is fluoro. In astill more preferred aspect, R¹⁰ and R¹² are hydrogen. Alternatively,R¹¹ and R¹² are hydrogen. In a yet still more preferred aspect, R¹⁰,R¹¹, and R¹² are hydrogen.

In a fourth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3-substituted with independently selected substituentsother than hydrogen, and the 1-substituent is the polymethine bridge(e.g., R⁸ is -L-Y—Z and R⁹ is alkyl; R⁸ is halo- and R⁹ is -L-Y—Z).Alternatively, the ring is 1,2,4-substituted. Alternatively, the ring is1,2,5-substituted. Alternatively, the ring is 1,2,6-substituted.Alternatively, the ring is 1,3,4-substituted. Alternatively, the ring is1,3,5-substituted. Alternatively, the ring is 1,3,6-substituted.

In a fifth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3,4-substituted with independently selected substituentsother than hydrogen, and the 1-substituent is the polymethine bridge.Alternatively, the ring is 1,2,3,5-substituted. Alternatively, the ringis 1,2,3,6-substituted. Alternatively, the ring is 1,2,4,5-substituted.Alternatively, the ring is 1,2,4,6-substituted. Alternatively, the ringis 1,2,5,6-substituted. Alternatively, the ring is 1,3,4,5-substituted.Alternatively, the ring is 1,3,4,6-substituted. Alternatively, the ringis 1,3,5,6-substituted.

In a sixth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3,4,5-substituted with independently selectedsubstituents other than hydrogen, and the 1-substituent is thepolymethine bridge. Alternatively, the ring is 1,3,4,5,6-substituted.Alternatively, the ring is 1,2,4,5,6-substituted. Alternatively, thering is 1,2,3,5,6-substituted. Alternatively, the ring is1,2,3,4,6-substituted. Alternatively, the ring is independentlysubstituted at each ring position.

In a seventh aspect, R⁸, R¹⁰, R¹¹, and R¹² are each a memberindependently selected from the group of hydrogen, alkyl, halo, andsulfonato.

In an eighth aspect, the combination of the phenyl ring and itssubstituents R⁸, R⁹, R¹⁰, R¹¹, and R¹² has at least ten carbons.

Fluoro substitution has been shown to increase quantum yield andphotostability in fluorescein dyes as well as lowering dye pK_(a) (seeSun, W.-C. et al. J. Org. Chem. 1997, 62, 6469-6475). In an eighthaspect, at least one member of the group R⁸, R⁹, R¹⁰, R¹¹, and R¹² is afluoro substituent. Alternatively, at least one member of the group R³,R⁴, R⁵, R⁶, and R¹⁴ is a fluoro substituent. In yet another aspect, atleast two members of R³, R⁴, R⁵, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ arefluoro substituents. In yet another aspect, at least three members ofR³, R⁴, R⁵, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², and R¹⁴ are fluoro substituents.

Each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl. In apreferred embodiment, R¹³ is carboxyl, amido, or alkoxycarbonyl. In amore preferred embodiment, R¹³ is carboxyl. Alternatively, R¹³ issulfonato. Alternatively, R¹³ is hydrogen.

Each R¹⁴ is a member independently selected from the group of alkyl,alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl; wherein the R¹⁴alkyl is additionally substituted with from 0 to 1 R¹³. Alternatively,each R¹⁴ is a member independently selected from the group of alkyl,alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl; wherein the R¹⁴alkyl is additionally substituted with from 0 to 2 R¹³. Alternatively,each R¹⁴ is a member independently selected from the group of alkyl,alkenyl, halo, hydrogen, hydroxyl, alkoxy, amino, cyano, carboxyl,alkoxycarbonyl, amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl;wherein the R¹⁴ alkyl is additionally substituted with from 0 to 2 R¹³.

In a preferred aspect, R¹⁴ is alkyl, alkenyl, carboxyl, alkoxycarbonyl,amido, or alkoxycarbonylalkyl. Alternatively, R¹⁴ is sulfonato.Alternatively, R¹⁴ is hydroxy. In a more preferred aspect, R¹⁴ is alkylor alkyl substituted with 1 R¹³. Alternatively, R¹⁴ is carboxyalkyl,hydroxyalkyl, or sulfonatoalkyl.

In one aspect, the R¹⁴ substituents are each independently, carboxy,carboxyalkyl, sulfonato, or sulfonatoalkyl. In a still more preferredaspect, the R¹⁴ substituents are each independently sulfonato orsulfonatoalkyl. In a yet more preferred aspect, each of the R¹⁴substituents is sulfonato.

Alternatively, each R¹⁴ is a member independently selected from thegroup of alkyl, alkenyl, halo, hydrogen, hydroxyl, alkoxy, amino, cyano,carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxycarbonylalkyl, andalkoxyalkyl; wherein the R¹⁴ alkyl is additionally substituted with from0 to 1 R¹³.

In one aspect, at least one pair of the R¹⁴ substituents is the same(i.e., the R^(n) substituent is not independently selected, but is thesame as the other R^(n) substituent). Alternatively, at least two pairsof the R¹⁴ substituents are the same. More preferably, the dye issymmetric or pseudo-symmetric (i.e., the R¹⁴ substituents on the dyeindoline rings are also not independently selected, but each R¹⁴substituent is the same as the analogous R¹⁴ substituents on the otherring).

In an alternative aspect, at least one R¹⁴ substituent is hydrogen.Alternatively, exactly R¹⁴ substituent is hydrogen. In a preferredaspect, at least one pair of R¹⁴ substituents is hydrogen.Alternatively, exactly two, exactly three, or exactly four R¹⁴substituents are hydrogen. In another aspect, exactly four R¹⁴substituents are hydrogen.

In another alternative aspect, at least one R¹⁴ substituent is sulfonatoor sulfonatoalkyl. Alternatively, exactly one R¹⁴ substituent issulfonato or sulfonatoalkyl. In still another aspect, at least one pairof R¹⁴ substituents is each a member independently selected from thegroup of sulfonato or sulfonatoalkyl. Alternatively, exactly one,exactly two, exactly three, or exactly four R¹⁴ substituents are each amember independently selected from the group of sulfonato orsulfonatoalkyl.

In another alternative aspect, at least one R¹⁴ substituent is anionicat physiological pH (e.g., sulfonato —SO₃ ⁻, carboxy —CO₂ ⁻).Alternatively, exactly one R¹⁴ substituent is anionic at physiologicalpH. In still another aspect, at least one pair of R¹⁴ substituents isanionic at physiological pH. Alternatively, exactly one, exactly two,exactly three, or exactly four R¹⁴ substituents are anionic atphysiological pH.

In an alternative aspect, at least one R¹⁴ substituent is zwitterionicat physiological pH (e.g., an alkyl group with anionic sulfonato —SO₃ ⁻and a cationic trialkylammonium group substituents). Alternatively,exactly one R¹⁴ substituent is zwitterionic at physiological pH. Instill another aspect, at least one pair of R¹⁴ substituents iszwitterionic at physiological pH. Alternatively, exactly one, exactlytwo, exactly three, or exactly four R¹⁴ substituents are zwitterionic atphysiological pH.

In another alternative aspect, at least one R¹⁴ substituent is halo.Alternatively, exactly one R¹⁴ substituent is halo. Alternatively,exactly two, exactly three, or exactly four R¹⁴ substituents are halo.

In one aspect, at least one pair of R¹, R^(2a), R^(2b), R³, R⁴, or R¹⁴is the same (i.e., the R^(n) substituent is not independently selected,but is the same as the other R^(n) substituent). This aspect can becombined with other aspects specifying the number or type of dyesubstituents (e.g., exactly two members of the groups R³, R⁴, and R¹⁴are hydrogen, and the two members are the pair of R⁴s). Alternatively,at least two, at least three, or all four pairs of R¹, R^(2a), R^(2b),R³, R⁴, or R¹⁴ are the same. More preferably, the dye is symmetric orpseudo-symmetric (i.e., R¹, R^(2a), and R^(2b) are also notindependently selected, but are the same as the other R¹, R^(2a), andR^(2b) substituents).

L is an optional member selected from the group of a bond, a C₁-C₁₀alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene or alkenylene isoptionally interrupted by at least one heteroatom. In a preferredaspect, L is not present. Alternatively, L is a C₁-C₁₀ alkyleneinterrupted by ether linkages (e.g., a polyethylene glycol oligomer).

Y is an optional member selected from the group of a bond, —O—, —S—,—NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—,—NZC(O)—, and —C(O)NZ—. In a preferred aspect, Y is a bond.Alternatively, Y is —O—. Alternatively, Y is an amido group optionallysubstituted with R¹⁵ at the amido nitrogen.

Each Z is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ and R¹⁶; wherein thealkyl is optionally interrupted by at least one heteroatom. In a morepreferred aspect, Z is C₁-C₆ alkyl. Alternatively, Z is interrupted byether linkages (e.g., a polyethylene glycol oligomer). In a still morepreferred aspect, Z is carboxyalkyl or sulfonatoalkyl. In a yet stillmore preferred aspect, Z is 5-carboxypentyl or 4-carboxybutyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R¹³; R¹³ is carboxyl or activated acyl; and t is an integerfrom 1 to 10, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. Alternatively, tis an integer from 0 to 10.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R¹³ or R¹⁶ that is directly bonded to thephenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastfour carbons. Alternatively, Z has at least four carbons.

R¹⁵ is a member selected from the group of alkyl andalkoxycarbonylalkyl; wherein the alkyl is optionally interrupted by atleast one heteroatom. In a preferred aspect, R¹⁵ is alkyl. In a morepreferred aspect, R¹⁵ is lower alkyl. Alternatively, R¹⁵ is interruptedby ether linkages (e.g., a polyethylene glycol oligomer).

Each R¹⁶ is independently a member selected from the group of activatedacyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl, isothiocyanato,iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl, and vinylsulfonyl. In a preferred aspect, R¹⁶ is activated acyl, maleimidyl,phosphoramidityl, or glycidyl. In a more preferred embodiment, R¹⁶ isactivated acyl. Alternatively, R¹⁶ is activated ester. In a still morepreferred embodiment, R¹⁶ is succinimidyloxy-ester orsulfosuccinimidyloxy-ester.

In an alternative embodiment that may incorporate one or more of theaspects described, the present invention provides a compound of FormulaIII′:

X is hydrogen, halo, alkyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl, alkenyl, or alkynyl. Preferably, X is hydrogen, halo, alkyl,or aryl. Preferably, X is or comprises an -L-Y—Z moiety. Alternatively,X is or comprises an R^(L) moiety.

In one embodiment of the oxidized state, the compound has a balancedcharge. In a preferred aspect, the compound's net anionic charge in theoxidized state is balanced by alkali metal counterions (e.g., sodium orpotassium). In a preferred aspect, in the oxidized state, at least oneof the counterions is sodium. Alternatively, all of the counterions aresodium.

In one embodiment, the compound's net cationic charge in the oxidizedstate is balanced by organic anions (e.g., acetate, chloride, sulfonate,or formate). In a preferred aspect, in the oxidized state, at least oneof the counterions is chloride or acetate. Alternatively, all of thecounterions are chloride or acetate.

The compound may also incorporate covalent bonds to both cationic andanionic groups to produce a balanced charge. Embodiments of suchcompounds are set forth in U.S. Patent Publication No. 2012/0028291,which is incorporated by reference. In a preferred aspect, thecompound's charge in the oxidized state is balanced by a combination ofalkali metal counterions (e.g., sodium or potassium) andtetraalkylammonium substituents (e.g., a trimethylammonium substituent;a triethylammonium substituent; or a methyl diethylammoniumsubstituent).

In a preferred aspect, the compound of Formula III has the formula:

Alternatively, in certain aspects, an activated acyl group is present inplace of the carboxy group. In a still more preferred aspect, theactivated acyl group is an activated ester. In a still yet morepreferred aspect, the activated ester is a succinimidyloxy-ester.

The compound of Formula III is substantially non-fluorescent, but uponoxidation fluoresces at a wavelength within the range of about 550 nm toabout 1000 nm. Preferably, the compound upon oxidation fluoresces at awavelength within the range of about 600 nm to about 850 nm. Morepreferably, the compound upon oxidation fluoresces at a wavelengthwithin the range of about 600 nm to about 725 nm. Alternatively, thecompound upon oxidation fluoresces at a wavelength within the range ofabout 725 nm to about 850 nm.

D. Compounds of Formula IV

In another embodiment, the present invention provides a compound ofFormula IVa or IVb:

Each R¹ is independently a member selected from the group consisting ofL-Y—Z and an alkyl group that is additionally substituted with from 0 to1 R¹³ and/or from 0 to 1 R¹⁶; wherein the alkyl is optionallyinterrupted by at least one heteroatom (e.g., an ethyl, such as in apoly(ethylene glycol)) or an ionic group (e.g., a charged alkylammoniumgroup, such as that in —CH₂(NMe₂)CH₂CH₂CH₂—).

In a preferred aspect, R¹ is C₁-C₂₀ alkyl. In a more preferred aspect,R¹ is C₁-C₁₂ or C₂-C₈ alkyl. In a still more preferred aspect, R¹ isC₂-C₆ alkyl. In a yet still more preferred aspect, R¹ is ethyl, propyl,butyl, or pentyl, and R¹ is additionally substituted with 1 R¹³.

In a preferred aspect, R¹ is not interrupted by a heteroatom.Alternatively, R¹ is interrupted by at least one ether, thioether,substituted amino, or amido group.

In another preferred aspect, R¹ is (CH₂)_(r)SO₃H or (CH₂)_(r)SO₃ ⁻; andr is an integer from 1 to 20. In a more preferred aspect, r is 2, 3, or4. Alternatively, R¹ is (CH₂)_(r)OH; and r is an integer from 2 to 6(e.g., 6-hydroxyhexyl).

In still another preferred aspect, R¹ is an alkyl group that isadditionally substituted with 1 R¹³ that is selected from the group ofhydroxyl, amino, carboxy, and sulfonato. In a more preferred aspect, theR¹³ substituent of R¹ is carboxy or sulfonato. In a still more preferredaspect, the R¹³ substituent of R¹ is sulfonato. In a yet still morepreferred aspect, R¹ is sulfonatoethyl, sulfonatopropyl, sulfonatobutyl,or sulfonatopentyl.

In yet another preferred aspect, R¹ is an unbranched alkyl group that isadditionally substituted with 1 R¹³. In a more preferred aspect, R¹ isan unbranched alkyl group that is substituted with R¹³ at the end of thealkyl group opposite to its attachment point to the reduced cyanine dyeheterocyclic nitrogen. In a still more preferred aspect, R¹ is2-sulfonatoethyl, 3-sulfonatopropyl, 4-sulfonatobutyl, or5-sulfonatopentyl. In a yet still more preferred aspect, R¹ is3-sulfonatopropyl or 4-sulfonatobutyl; more preferably, R¹ is3-sulfonatopropyl.

R^(1a) is either hydrogen or deuterium. Alternatively, R^(1a′) istritium.

In still another preferred aspect, R¹ is L-Y—Z. For example, L is aC₁-C₂₀ alkylene group such as C₂-C₈ alkylene; Y is a C(O)NH group; and Zis L-R¹⁶, wherein L is a C₁-C₂₀ alkylene group such as C₂-C₈ alkyleneand R¹⁶ is a cycloalkynylcarbonyl like C(O)DBCO (see for example,compound 66). In another aspect, R¹ is L-Y—Z, wherein L is a C₁-C₂₀alkylene group such as C₂-C₈ alkylene; Y is a C(O)NH group; and Z isL-R¹⁶, wherein L is a C₁-C₂₀ alkylene group such as C₂-C₈ alkyleneoptionally interrupted by a heteroatom (e.g., ((CH₂CH₂O)₃—CH₂CH₂—) andR¹⁶ is an azido group).

Each R^(2a) and R^(2b) is a member independently selected from the groupconsisting of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl,amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, orsulfonatoalkyl; wherein a carbon of the member is additionallysubstituted with from 0 to 1 R¹⁶.

In a preferred aspect, all R^(2a) are the same substituent.Alternatively, all R^(2b) are the same substituent. More preferably, allR^(2a) are the same substituent, and all R^(2b) are the samesubstituent.

In another preferred aspect, R^(2a) and R^(2b) are the same. In a morepreferred aspect, R^(2a) and R^(2b) are alkyl, alkenyl, aminoalkyl,carboxyalkyl, or sulfonatoalkyl. In a still more preferred aspect,R^(2a) and R^(2b) are alkyl, carboxyalkyl, or sulfonatoalkyl. In a yetstill more preferred aspect, R^(2a) and R^(2b) are methyl.

In an alternative aspect, R^(2a) and R^(2b) are different. In a morepreferred aspect, R^(2a) is alkyl, and R^(2b) is selected from the groupof alkyl, alkenyl, aminoalkyl, carboxyalkyl, or sulfonatoalkyl. In astill more preferred aspect, R^(2a) is alkyl, and R^(2b) is selectedfrom the group of alkyl, carboxyalkyl, or sulfonatoalkyl. Yet still morepreferably, R^(2a) is methyl.

Each R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) is a memberindependently selected from the group consisting of hydrogen, alkyl,alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, andsulfonatoalkyl; wherein a carbon of the member is additionallysubstituted with from 0 to 1 R¹⁶.

In a first aspect, each R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), andR^(6b) is a member independently selected from the group consisting ofhydrogen, alkyl, alkenyl, halo, alkoxy, cyano, carboxyl, alkoxycarbonyl,amido, sulfonato, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, andsulfonatoalkyl. In a preferred aspect, each R³, R^(4a), R^(4b), R^(5a),R^(5b), R^(6a), and R^(6b) is a member independently selected from thegroup of hydrogen, alkyl, carboxy, carboxyalkyl, halo, sulfanato, andsulfanatoalkyl. In a more preferred embodiment, each R³, R^(4a), R^(4b),R^(5a), R^(5b), R^(6a), and R^(6b) is a member independently selectedfrom the group of hydrogen, halo, and sulfanato.

In an alternative aspect, at least one member of the group R³, R^(4a),R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) is hydrogen. Alternatively,exactly one member of the group R³, R^(4a), R^(4b), R^(5a), R^(5b),R^(6a), and R^(6b) is hydrogen. In a preferred aspect, at least one pairof substituents selected from the pairs R³ and R^(4a); R³ and R^(5a); R³and R^(6a); R^(4a) and R^(5a); R^(4a) and R^(6a); R^(5a) and R^(6a), R³and R^(4b); R³ and R^(5b); R³ and R^(6b); R^(4b) and R^(5b); R^(4b) andR^(6b); and R^(5b) and R^(6b) is hydrogen. Alternatively, exactly two,exactly three, exactly four, exactly five, or exactly six members of thegroup R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) arehydrogen. In a more preferred aspect, exactly four members of the groupR³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) are hydrogen.Alternatively, exactly five members of the group R³, R^(4a), R^(4b),R^(5a), R^(5b), R^(6a), and R^(6b) are hydrogen. In a still morepreferred aspect, R³, R^(4a), R^(6a), R^(4b), and R^(6b) are hydrogen.

In another alternative aspect, at least one member of the group R³,R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) is sulfonato orsulfonatoalkyl. Alternatively, exactly one substituent selected from thegroup R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) issulfonato or sulfonatoalkyl. In a preferred aspect, R^(5a) is sulfonato.In still another aspect, both members of a pair of substituents selectedfrom the pairs R³ and R^(4a); R³ and R^(5a); R³ and R^(6a); R^(4a) andR^(5a); R^(4a) and R^(6a); R^(5a) and R^(6a), R³ and R^(4b); R³ andR^(5b); R³ and R^(6b); R^(4b) and R^(5b); R^(4b) and R^(6b); and R^(5b)and R^(6b) are each a member independently selected from the group ofsulfonato or sulfonatoalkyl. Alternatively, exactly two, exactly three,exactly four, exactly five, or exactly six members of the group R³,R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) are each a memberindependently selected from the group of sulfonato or sulfonatoalkyl.

In another alternative aspect, at least one member of the group R³,R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and R^(6b) is anionic atphysiological pH (e.g., sulfonato —SO₃ ⁻, carboxyl —CO₂ ⁻).Alternatively, exactly one member of the group R³, R^(4a), R^(4b),R^(5a), R^(5b), R^(6a), and, and R^(6b) is anionic at physiological pH.In a preferred aspect, R^(5a) is anionic at physiological pH. In stillanother aspect, each member of a pair of substituents selected from thepairs R³ and R^(4a); R³ and R^(5a); R³ and R^(6a); R^(4a) and R^(5a);R^(4a) and R^(6a); R^(5a) and R^(6a), R³ and R^(4b); R³ and R^(5b); R³and R^(6b); R^(4b) and R^(5b); R^(4b) and R^(6b); and R^(5b) and R^(6b)is anionic at physiological pH. Alternatively, exactly two, exactlythree, exactly four, exactly five, or exactly six members of the groupR³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and, and R^(6b) are anionicat physiological pH. exactly two, exactly three, or exactly four membersof the group R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a) and, and R^(6b)are anionic at physiological pH.

In another alternative aspect, at least one member of the group R³,R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and, and R^(6b) is halo.Alternatively, exactly one substituent selected from the group R³,R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and, and R^(6b) is halo. In apreferred aspect, R^(5b) is halo; more preferably, R^(5b) is chloro. Instill another aspect, both members of a pair of substituents selectedfrom the pairs R³ and R^(4a); R³ and R^(5a); R³ and R^(6a); R^(4a) andR^(5a); R^(4a) and R^(6a); R^(5a) and R^(6a), R³ and R^(4b); R³ andR^(5b); R³ and R^(6b); R^(4b) and R^(5b); R^(4b) and R^(6b); R^(5b) andR^(6b) are each an independently selected halo. Alternatively, exactlytwo, exactly three, exactly four, exactly five, or exactly six membersof the group R³, R^(4a), R^(4b), R^(5a), R^(5b), R^(6a), and, and R^(6b)are each an independently selected halo.

R⁸, R⁹, R¹⁰, R¹¹ and R¹² are each a member independently selected fromthe group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy,sulfonato, sulfonatoalkyl, hydroxyl, amino, carboxyl, alkoxycarbonyl,cyano, amido, thioacetyl, and -L-Y—Z; wherein, if present, at least onemember selected from the group consisting of R⁸, R⁹, and R¹⁰ is -L-Y—Z.

In one aspect, R⁸ is -L-Y—Z. Preferably, R⁹, R¹⁰, R¹¹, and R¹² are eacha member independently selected from the group consisting of hydrogen,alkyl, halo, sulfonato, and sulfonatoalkyl.

In a second aspect, R⁸ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R⁸ is hydrogen.

Alternatively, R⁸ is a carboxyalkyl. Preferably, R⁸ is a lower alkylgroup with a carboxyl substituent. More preferably, R⁸ is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, R⁸ is 5-carboxypentyl or2-carboxyethyl.

Alternatively, R⁸ is carboxyl, alkoxycarbonyl, or amido; morepreferably, R⁸ is carboxyl.

In one aspect, R¹⁰ is -L-Y—Z. Preferably, R⁸, R⁹, R¹¹, and R¹² are eacha member independently selected from the group consisting of hydrogen,alkyl, halo, sulfonato, and sulfonatoalkyl.

In a second aspect, R¹⁰ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹⁰ is hydrogen.

Alternatively, R¹⁰ is a carboxyalkyl. Preferably, R¹⁰ is a lower alkylgroup with a carboxyl substituent. More preferably, R¹⁰ is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, R¹⁰ is 5-carboxypentyl or2-carboxyethyl.

Alternatively, R¹⁰ is carboxyl, alkoxycarbonyl, or amido; morepreferably, R¹⁰ is carboxyl.

In one aspect, R⁹ is -L-Y—Z. Preferably, R⁸, R¹⁰, R¹¹, and R¹² are eacha member independently selected from the group consisting of hydrogen,alkyl, halo, sulfonato, and sulfonatoalkyl.

In a second aspect, R⁹ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R⁹ is hydrogen.

Alternatively, R⁹ is a carboxyalkyl. Preferably, R⁹ is a lower alkylgroup with a carboxyl substituent. More preferably, R⁹ is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, R⁹ is 5-carboxypentyl or2-carboxyethyl.

Alternatively, R⁹ is carboxyl, alkoxycarbonyl, or amido; morepreferably, R⁹ is carboxyl.

In one aspect, R¹¹ and R¹² are each a member independently selected fromthe group of hydrogen, alkyl, alkenyl, halo, alkoxy, sulfonato,hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido, thioacetyl, and-L-Y—Z. Preferably, R¹¹ and R¹² are each a member independently selectedfrom the group of hydrogen, alkyl, halo, sulfonato, and sulfonatoalkyl.More preferably, R¹¹ and R¹² are each a member independently selectedfrom the group of hydrogen, halo, and sulfonato.

In a second aspect, R¹¹ is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹¹ is hydrogen. In a still more preferred aspect, R¹⁰and R¹¹ are hydrogen.

In a third aspect, R¹² is hydrogen, alkyl, alkoxy, or halo. In a morepreferred aspect, R¹² is hydrogen. In a still more preferred aspect, R¹⁰and R¹² are hydrogen. Alternatively, R¹¹ and R¹² are hydrogen. In a yetstill more preferred aspect, R¹⁰, R¹¹, and R¹² are hydrogen.

In a fourth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3-substituted with independently selected substituentsother than hydrogen, and the 1-substituent is the polymethine bridge(e.g., R⁸ is -L-Y—Z and R⁹ is alkyl; R⁸ is halo- and R⁹ is -L-Y—Z).Alternatively, the ring is 1,2,4-substituted. Alternatively, the ring is1,2,5-substituted. Alternatively, the ring is 1,2,6-substituted.Alternatively, the ring is 1,3,4-substituted. Alternatively, the ring is1,3,5-substituted. Alternatively, the ring is 1,3,6-substituted.

In a fifth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3,4-substituted with independently selected substituentsother than hydrogen, and the 1-substituent is the polymethine bridge.Alternatively, the ring is 1,2,3,5-substituted. Alternatively, the ringis 1,2,3,6-substituted. Alternatively, the ring is 1,2,4,5-substituted.Alternatively, the ring is 1,2,4,6-substituted. Alternatively, the ringis 1,2,5,6-substituted. Alternatively, the ring is 1,3,4,5-substituted.Alternatively, the ring is 1,3,4,6-substituted. Alternatively, the ringis 1,3,5,6-substituted.

In a sixth aspect, the phenyl ring substituted with R⁸, R⁹, R¹⁰, R¹¹,and R¹² is 1,2,3,4,5-substituted with independently selectedsubstituents other than hydrogen, and the 1-substituent is thepolymethine bridge. Alternatively, the ring is 1,3,4,5,6-substituted.Alternatively, the ring is 1,2,4,5,6-substituted. Alternatively, thering is 1,2,3,5,6-substituted. Alternatively, the ring is1,2,3,4,6-substituted. Alternatively, the ring is independentlysubstituted at each ring position.

In a seventh aspect, R⁸, R¹⁰, R¹¹, and R¹² are each a memberindependently selected from the group of hydrogen, alkyl, halo,sulfonato, and sulfonatoalkyl.

In an eighth aspect, the combination of the phenyl ring and itssubstituents R⁸, R⁹, R¹⁰, R¹¹, and R¹² has at least ten carbons.

Each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl. In apreferred embodiment, R¹³ is carboxyl, amido, or alkoxycarbonyl. In amore preferred embodiment, R¹³ is carboxyl. Alternatively, R¹³ issulfonato.

Each L is an optional member independently selected from the groupconsisting of a bond, a C₁-C₂₀ alkylene, and a C₁-C₂₀ alkenylene;wherein the alkylene or alkenylene is optionally interrupted by at leastone heteroatom. In a preferred aspect, L is a bond. Alternatively, L isa C₁-C₁₄ alkylene; more preferably, L is a C₁-C₁₀ alkylene or a C₁-C₆alkylene. Alternatively, L is a C₁-C₁₂ alkylene interrupted by etherlinkages (e.g., a polyethylene glycol oligomer).

In a preferred aspect, the alkylene or alkenylene is not interrupted bya heteroatom. Alternatively, L is interrupted by at least one ether,thioether, substituted amino, or amido group.

Each Y is an optional member independently selected from the groupconsisting of a bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—,—NR¹⁵C(O)—, —C(O)NR¹⁵—, —N(Z)—, —N(Z)C(O)—, and —C(O)N(Z)—. In apreferred aspect, Y is a bond. Alternatively, Y is —O—. Alternatively, Yis an amido group optionally substituted with R¹⁵ at the amido nitrogen.

Each Z is independently selected from the group consisting of -L-R¹³ and-L-R¹⁶. In a preferred aspect, the -L- is a C₁-C₂₀ alkylene; morepreferably, a C₁-C₁₂ alkylene; and still more preferably, a C₁-C₁₀alkylene. Alternatively, the -L- is a bond. Yet still more preferably,the -L- is C₁-C₆ alkyl. Alternatively, the -L- is interrupted by etherlinkages (e.g., a polyethylene glycol oligomer). In a still morepreferred aspect, Z is carboxyalkyl or sulfonatoalkyl. In a yet stillmore preferred aspect, Z is 5-carboxypentyl or 4-carboxybutyl.

In an alternative preferred aspect, Z is a carboxyalkyl. Preferably, Zis a lower alkyl group with a carboxy-substituent. More preferably, Z is5-carboxypentyl, 4-carboxybutyl, 3-carboxypropyl, 2-carboxyethyl, orcarboxymethyl. Still more preferably, Z is 5-carboxypentyl or2-carboxyethyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R¹³, R¹³ is carboxyl or activated acyl; and t is an integerfrom 0 to 10, such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.Alternatively, t is an integer from 1 to 10.

In still another alternative preferred aspect, -L-Y— is a bond. Morepreferably, Z is directly bonded to the phenyl ring or the polymethylenebridge.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R¹³ or R¹⁶ that is directly bonded to thephenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastthree carbons. Alternatively, Z has at least three carbons.

In an alternative embodiment, —Y—Z is a member selected from the groupconsisting of —N(Z)₂, —N(Z)C(O)Z, and —C(O)N(Z)₂, and the two Z groupsmay optionally be linked to form a cycloalkynyl group

Each R¹⁵ is a member independently selected from the group consisting ofalkyl and alkoxycarbonylalkyl; wherein the alkyl is optionallyinterrupted by at least one heteroatom. In a preferred aspect, R¹⁵ isalkyl. In a more preferred aspect, R¹⁵ is lower alkyl. Alternatively,R¹⁵ is interrupted by ether linkages (e.g., a polyethylene glycololigomer).

In a preferred aspect, the alkyl is not interrupted by a heteroatom. Ina preferred aspect, R¹⁵ is alkyl. In a more preferred aspect, R¹⁵ islower alkyl.

Alternatively, L is interrupted by at least one ether, thioether,substituted amino, or amido group. Preferably, R¹⁵ is interrupted by atleast one ether group (e.g., a polyethylene glycol oligomer).

Each R¹⁶ is independently a member selected from the group consisting ofactivated acyl, acrylamido, optionally substituted alkylsulfonate ester,azido, optionally substituted arylsulfonate ester, optionallysubstituted amino, aziridino, boronato, cycloalkynyl,cycloalkynylcarbonyl, diazo, formyl, glycidyl, halo, haloacetamidyl,haloalkyl, haloplatinato, halotriazino, hydrazinyl, imido ester,isocyanato, isothiocyanato, maleimidyl, mercapto, phosphoramidityl, aphotoactivatable moiety, vinyl sulfonyl, alkynyl, a pegylated azido, apegylated alkynyl, a pegylated cycloalkynyl, an ortho substitutedphosphinyl aryl ester (e.g., TPPME), a spirocycloalkynyl, and an orthosubstituted phosphine oxide aryl ester.

The oxidized form of the compound has a balanced charge. In a preferredaspect, the oxidized compound's net anionic charge is balanced by alkalimetal counterions (e.g., sodium or potassium). In a more preferredaspect, at least one of the counterions is sodium. Alternatively, all ofthe counterions are sodium.

In a more preferred aspect, the compound of Formula IVa or IVb has theformula:

wherein M is a cationic counterion. More preferably, M is an alkalimetal ion.

In certain aspects, an activated acyl group is present in place of thecarboxy group. In a still more preferred aspect, the activated acylgroup is an activated ester. In a still yet more preferred aspect, theactivated ester is a succinimidyloxy-ester.

In a first aspect, the oxidized state of the compound of Formula IVa orIVb has a fluorescence absorption maximum at a wavelength within therange of about 550 nm to about 1000 nm. Preferably, the oxidized stateof the compound has a fluorescence absorption maximum at a wavelengthwithin the range of about 600 nm to about 1000 nm. More preferably, theoxidized state of the compound has a fluorescence absorption maximum ata wavelength within the range of about 600 nm to about 850 nm. Stillmore preferably, the oxidized state of the compound has a fluorescenceabsorption maximum at a wavelength within the range of about 600 nm toabout 725 nm. Alternatively, the oxidized state of the compound has afluorescence absorption maximum at a wavelength within the range ofabout 725 nm to about 850 nm.

In some embodiments, the parent compound's oxidized form has a balancedcharge. In a preferred aspect, the compound's net anionic charge in theoxidized state is balanced by alkali metal counterions (e.g., sodium orpotassium). In a preferred aspect, in the parent compound's oxidizedstate, at least one of the counterions is sodium. Alternatively, all ofthe counterions are sodium.

In one embodiment, the compound's net cationic charge in the oxidizedstate is balanced by organic anions (e.g., acetate, chloride, sulfonate,orformate). In a preferred aspect, in the parent compound's oxidizedstate, at least one of the counterions is chloride or acetate.Alternatively, all of the counterions are chloride or acetate.

The compound may also incorporate covalent bonds to both cationic andanionic groups to produce a balanced charge. Embodiments of suchcompounds are set forth in U.S. Patent Publication No. 2012/0028291,which is incorporated by reference. In a preferred aspect, thecompound's charge in the oxidized state is balanced by a combination ofalkali metal counterions (e.g., sodium or potassium) andtetraalkylammonium substituents (e.g., a trimethylammonium substituent;a triethylammonium substituent; or a methyl diethylammoniumsubstituent).

E. Compounds of Formula V

In another embodiment, the present invention provides a compound ofFormula V:

Each R¹ is independently a member selected from the group consisting ofL-Y—Z and an alkyl group that is additionally substituted with from 0 to1 R¹³ and from 0 to 1 R¹⁶; wherein the alkyl is optionally interruptedby at least one heteroatom (e.g., an ethyl, such as in a poly(ethyleneglycol)) or an ionic group (e.g., a charged alkylammonium group, such asthat in —CH₂(NMe₂)CH₂CH₂CH₂—).

In a preferred aspect, R¹ is C₁-C₂₀ alkyl. In a more preferred aspect,R¹ is C₁-C₁₂ or C₂-C₈ alkyl. In a still more preferred aspect, R¹ isC₂-C₆ alkyl. In a yet still more preferred aspect, R¹ is ethyl, propyl,butyl, or pentyl, and R¹ is additionally substituted with 1 R¹³.

In a preferred aspect, R¹ is not interrupted by a heteroatom.Alternatively, R¹ is interrupted by at least one ether, thioether,substituted amino, or amido group.

In another preferred aspect, R¹ is (CH₂)_(r)SO₃H or (CH₂)_(r)SO₃ ⁻; andr is an integer from 1 to 20. In a more preferred aspect, r is 2, 3, or4. Alternatively, R¹ is (CH₂)_(r)OH; and r is an integer from 2 to 6(e.g., 6-hydroxyhexyl).

In still another preferred aspect, R¹ is an alkyl group that isadditionally substituted with 1 R¹³ that is selected from the group ofhydroxyl, amino, carboxy, and sulfonato. In a more preferred aspect, theR¹³ substituent of R¹ is carboxy or sulfonato. In a still more preferredaspect, the R¹³ substituent of R¹ is sulfonato. In a yet still morepreferred aspect, R¹ is sulfonatoethyl, sulfonatopropyl, sulfonatobutyl,or sulfonatopentyl.

In yet another preferred aspect, R¹ is an unbranched alkyl group that isadditionally substituted with 1 R¹³. In a more preferred aspect, R¹ isan unbranched alkyl group that is substituted with R¹³ at the end of thealkyl group opposite to its attachment point to the reduced cyanine dyeheterocyclic nitrogen. In a still more preferred aspect, R¹ is2-sulfonatoethyl, 3-sulfonatopropyl, 4-sulfonatobutyl, or5-sulfonatopentyl. In a yet still more preferred aspect, R¹ is3-sulfonatopropyl or 4-sulfonatobutyl; more preferably, R¹ is3-sulfonatopropyl.

R^(1a) is either hydrogen or deuterium. Alternatively, R^(1a′) istritium.

Each R¹³ is a member independently selected from the group of hydroxyl,amino, carboxyl, alkoxycarbonyl, amido, sulfonato, and thioacetyl. In apreferred embodiment, R¹³ is carboxyl, amido, or alkoxycarbonyl. In amore preferred embodiment, R¹³ is carboxyl. Alternatively, R¹³ issulfonato.

L is an optional member selected from the group of a bond, a C₁-C₁₀alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene or alkenylene isoptionally interrupted by at least one heteroatom. In a preferredaspect, L is not present. Alternatively, L is a C₁-C₁₀ alkyleneinterrupted by ether linkages (e.g., a polyethylene glycol oligomer).

Y is an optional member selected from the group of a bond, —O—, —S—,—NH—, —NHC(O)—, —C(O)NH—, —NR¹⁵—, —NR¹⁵C(O)—, —C(O)NR¹⁵—, —NZ—,—NZC(O)—, and —C(O)NZ—. In a preferred aspect, Y is a bond.Alternatively, Y is —O—. Alternatively, Y is an amido group optionallysubstituted with R¹⁵ at the amido nitrogen.

Each Z is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ and R¹⁶; wherein thealkyl is optionally interrupted by at least one heteroatom. In a morepreferred aspect, Z is C₁-C₆ alkyl. Alternatively, Z is interrupted byether linkages (e.g., a polyethylene glycol oligomer). In a still morepreferred aspect, Z is carboxyalkyl or sulfonatoalkyl. In a yet stillmore preferred aspect, Z is 5-carboxypentyl or 4-carboxybutyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R¹³; R¹³ is carboxyl or activated acyl; and t is an integerfrom 1 to 10 such as 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. Alternatively, tis an integer from 0 to 10.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R¹³ or R¹⁶ that is directly bonded to thephenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastfour carbons. Alternatively, Z has at least four carbons.

R¹⁵ is a member selected from the group of alkyl andalkoxycarbonylalkyl; wherein the alkyl is optionally interrupted by atleast one heteroatom. In a preferred aspect, R¹⁵ is alkyl. In a morepreferred aspect, R¹⁵ is lower alkyl. Alternatively, R¹⁵ is interruptedby ether linkages (e.g., a polyethylene glycol oligomer).

Each R¹⁶ is independently a member selected from the group of activatedacyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl, isothiocyanato,iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl, and vinylsulfonyl. In a preferred aspect, R¹⁶ is activated acyl, maleimidyl,phosphoramidityl, or glycidyl. In a more preferred embodiment, R¹⁶ isactivated acyl. Alternatively, R¹⁶ is activated ester. In a still morepreferred embodiment, R¹⁶ is succinimidyloxy-ester orsulfosuccinimidyloxy-ester.

In one embodiment, the compound of Formula V has the formula:

In still other embodiments, the present invention provides the followingcompounds:

wherein X is hydrogen, halo, alkyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl, alkenyl, or alkynyl. Preferably, X is hydrogen, halo, alkyl,or aryl. Preferably, X is or comprises an -L-Y—Z moiety. Alternatively,X is or comprises an R^(L) moiety. Alternatively, X is or comprises anionic group (e.g., a charged alkylammonium group, such as that in—CH₂(NMe₃)).

F. Compounds of Formula VI

Hydrocyanine and deuterocyanine dyes as described in U.S. PatentApplication Publication No. 2011/0070166 can be used in the methods ofthe invention. In some embodiments, for example, thehydro/deteurocyanine dye is a compound according to Formula VI (a):

-   -   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R        is C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are        independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;        —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where        R is as defined above; or —CONR¹³R¹⁴, wherein R¹³ and R¹⁴ are        independently hydrogen or R as defined above;    -   R¹-R⁴ are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfate, C₁₋₂₀ alkyl carboxylate; C₁₋₂₀ alkyl amino; aryl,        benzyl, oligoethylene glycol, L-Y—Z, an ionic group, or        polyethylene glycol;    -   R⁵ and R⁶ are independently hydrogen; hydroxyl; —OR⁸; —NH₂;        —NHR⁹; —NR¹⁰R¹¹, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfonate, C₁₋₂₀ alkyl        carboxylic acid or carboxylate; C₁₋₂₀ alkyl amino or quaternized        amino; —COOH; —CO₂ ⁻ or —SO₃ ⁻; wherein R⁸-R¹¹ are independently        R as defined above; oligoethylene glycol, or polyethylene        glycol;    -   n is an integer from 1-5;    -   R¹² is H or D;    -   L is an optional member selected from the group of a bond, a        C₁-C₁₀ alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene        or alkenylene is optionally interrupted by at least one        heteroatom;    -   Y is an optional member selected from the group of a bond, —O—,        —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR^(15′)—, —NR^(15′)C(O)—,        —C(O)NR^(15′)—, —NZ—, —NZC(O)—, and —C(O)NZ—;    -   each Z is an independently selected C₁-C₁₀ alkyl that is        additionally substituted with one member from the group of        R^(13′) and R^(16′); wherein the alkyl is optionally interrupted        by at least one heteroatom;    -   each R^(13′) is a member independently selected from the group        of hydroxyl, amino, carboxyl, alkoxycarbonyl, amido, sulfonato,        and thioacetyl    -   each R^(15′) is a member independently selected from the group        of alkyl and alkoxycarbonylalkyl; wherein the alkyl is        optionally interrupted by at least one heteroatom; and    -   each R^(16′) is independently a member selected from the group        of activated acyl, formyl, glycidyl, halo, haloalkyl,        hydrazidyl, isothiocyanato, iodoacetamidyl, maleimidyl,        mercapto, phosphoramidityl, and vinyl sulfonyl.

In some embodiments, L is an optional member selected from the group ofa bond, a C₁-C₁₀ alkylene, and a C₁-C₁₀ alkenylene; wherein the alkyleneor alkenylene is optionally interrupted by at least one heteroatom orionic group. In a preferred aspect, L is not present. Alternatively, Lis a C₁-C₁₀ alkylene interrupted by ether linkages (e.g., a polyethyleneglycol oligomer).

In some embodiments, Y is an optional member selected from the group ofa bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR^(15′)—, —NR^(15′)C(O)—,—C(O)NR^(15′)—, —NZ—, —NZC(O)—, and —C(O)NZ—. In a preferred aspect, Yis a bond. Alternatively, Y is —O—. Alternatively, Y is an amido groupoptionally substituted with R^(15′) at the amido nitrogen.

In some embodiments, each Z is an independently selected C₁-C₁₀ alkylthat is additionally substituted with one member from the group ofR^(13′) and R^(16′); wherein the alkyl is optionally interrupted by atleast one heteroatom or ionic group. In a more preferred aspect, Z isC₁-C₆ alkyl. Alternatively, Z is interrupted by ether linkages (e.g., apolyethylene glycol oligomer). In a still more preferred aspect, Z iscarboxyalkyl or sulfonatoalkyl. In a yet still more preferred aspect, Zis 5-carboxypentyl or 4-carboxybutyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R^(13′); R^(13′) is carboxyl or activated acyl; and t is aninteger from 1 to 10 such as 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.Alternatively, t is an integer from 0 to 10.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R^(13′) or R^(16′) that is directly bondedto the phenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastfour carbons. Alternatively, Z has at least four carbons.

Each R^(13′) is a member independently selected from the group ofhydroxyl, amino, carboxyl, alkoxycarbonyl, amido, sulfonato, andthioacetyl. In a preferred embodiment, R^(13′) is carboxyl, amido, oralkoxycarbonyl. In a more preferred embodiment, R^(13′) is carboxyl.Alternatively, R^(13′) is sulfonato.

In some embodiments, each R^(15′) is a member independently selectedfrom the group of alkyl and alkoxycarbonylalkyl; wherein the alkyl isoptionally interrupted by at least one heteroatom or ionic group. In apreferred aspect, R^(15′) is alkyl. In a more preferred aspect, R^(15′)is lower alkyl. Alternatively, R¹ is interrupted by ether linkages(e.g., a polyethylene glycol oligomer).

Each R^(16′) is independently a member selected from the group ofactivated acyl, formyl, glycidyl, halo, haloalkyl, hydrazidyl,isothiocyanato, iodoacetamidyl, maleimidyl, mercapto, phosphoramidityl,and vinyl sulfonyl. In a preferred aspect, R^(16′) is activated acyl,maleimidyl, phosphoramidityl, or glycidyl. In a more preferredembodiment, R^(16′) is activated acyl. Alternatively, R^(16′) is anactivated ester. In a still more preferred embodiment, R^(16′) issuccinimidyloxy-ester or sulfosuccinimidyloxy-ester; and the benzenering represented by dotted lines is optional.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (b):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO2;    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is as defined above; or —CONR¹²R¹³, wherein R¹² and R¹³ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR⁷; —NH₂;        —NHR⁸; —NR⁹R¹⁰, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO2⁻ or —SO3.⁻; wherein        R⁷-R¹⁰ are independently R as defined above; oligoethylene        glycol, or polyethylene glycol;    -   n is an integer from 1-5;    -   R¹¹ is H or D, and    -   the benzene ring represented by dotted lines is optional.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (c):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹²R¹³, wherein R¹² and R¹³ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR⁷; —NH₂;        —NHR⁸; —NR⁹R¹⁰, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO₂.⁻ or —SO₃ ⁻; wherein        R⁷-R¹⁰ are independently R as defined above; oligoethylene        glycol, or polyethylene glycol;    -   n is an integer from 1-5;    -   R¹¹ is H or D; and    -   the fused phenyl ring represented by dotted lines is optional.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (d):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂,    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹⁷R¹⁸, wherein R¹⁷ and R¹⁸ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR¹²; —NHR¹³;        —NR¹⁴R¹⁵, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO₂ ⁻ or —SO₃ ⁻; wherein        R¹²-R¹⁵ are independently R as defined above; oligoethylene        glycol, or polyethylene glycol;    -   R⁵-R⁸ are independently hydrogen or C₁₋₂₀ alkyl;    -   n is an integer from 1-5;    -   R¹⁶ is H or D; and    -   the benzene ring represented by dotted lines is optional,        wherein if the benzene ring is not present, R¹⁶ is D.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (e):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂,    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹⁶R¹⁷, wherein R¹⁶ and R¹⁷ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR¹¹; —NHR¹²;        —NR¹³R¹⁴, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO₂ ⁻ or —SO₃ ⁻; wherein        R¹¹-R¹⁴ are independently R as defined above; oligoethylene        glycol, or polyethylene glycol;    -   R⁵-R⁸ are independently hydrogen or C₁₋₂₀ alkyl;    -   R¹⁵ is H or D; and    -   n is an integer from 1-5.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (f):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹²R¹³, wherein R¹² and R¹³ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR⁷; —NHR⁸;        —NR⁹R¹⁰, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; oligoethylene glycol, or        polyethylene glycol; —COOH; —CO₂ ⁻ or —SO₃ ⁻; wherein R⁷-R¹⁰ are        independently R as defined above;    -   R¹¹ is H or D; and    -   n is an integer from 1-5.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (g):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹²R¹³, wherein R¹² and R¹³ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol; and    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR⁷; —NHR⁸;        —NR⁹R¹⁰, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO₂ ⁻ or —SO₃ ⁻; wherein        R⁷-R¹⁰ are independently R as defined above; oligoethylene        glycol, or polyethylene glycol;    -   n is an integer from 1-5; and    -   q is 0, 1, or 2.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to formula VI (h):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹²R¹³, wherein R¹² and R¹³ are    independently hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol; and    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR⁷; —NHR⁸;        —NR⁹R¹⁰, C₁₋₂₀ alkyl, C₁₋₂₀ alkyl sulfate, C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO₂ ⁻ or —SO₃—; wherein        R⁷-R¹⁰ are independently R as defined above; oligoethylene        glycol, or polyethylene glycol;    -   R¹¹ is D; and    -   n is an integer from 1-5.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to Formula VI (i):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;    —S—C₁₋₂₀ alkyl; —S-aryl; aryl, —COOH; —COH; —COR or —COOR, where R    is defined above; or —CONR¹³R¹⁴, wherein R¹³ and R¹⁴ are    independently hydrogen or R as defined above;    -   R¹-R⁴ are independently hydrogen, C₁₋₂₀ alkyl; C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R⁵ and R⁶ are independently hydrogen; hydroxyl; —OR⁵; —NH₂;        —NHR⁶; —NR⁷R⁸, C₁₋₂₀ alkyl; C₁₋₂₀ alkyl sulfate; C₁₋₂₀ alkyl        carboxylate; C₁₋₂₀ alkyl amino; —COOH; —CO₂ ⁻; or —SO₃ ⁻;        wherein R⁵-R⁸ are independently R as defined above;        oligoethylene glycol, or polyethylene glycol;    -   Y and Z are independently carbon, nitrogen or sulfur, wherein if        Y and/or Z is carbon, the carbon is tetravalent having two        substituents as defined above; if Y and/or Z is sulfur; the        sulfur is divalent; and if Y and/or Z is nitrogen, the nitrogen        is trivalent, having one substituent as defined above;    -   R¹² is H or D; and    -   the benzene ring represented by dotted lines is optional.

In some embodiments, the hydro/deteurocyanine dye used in the methods ofthe invention is a compound according to formula VI (j):

-   wherein X is hydrogen; halogen; C₁₋₂₀ alkyl; aryl; —OR, where R is    C₁₋₂₀ alkyl or aryl; hydroxyl; —NR⁵R⁶, where R⁵ and R⁶ are    independently hydrogen, C₁₋₂₀ alkyl or aryl; —CN, —SH; —NO₂;    —S—C₁₋₂₀ alkyl; —S-aryl; —COOH; —COH; —COR or —COOR, where R is    defined above; or —CONR¹³R¹⁴, wherein R¹³ and R¹⁴ are independently    hydrogen or R as defined above;    -   R¹ and R² are independently hydrogen, C₁₋₂₀ alkyl; C₁₋₂₀ alkyl        sulfonate, C₁₋₂₀ alkyl carboxylic acid or carboxylate; C₁₋₂₀        alkyl amino or quaternized amino; aryl, benzyl, oligoethylene        glycol, L-Y—Z (as defined in VIa), an ionic group, or        polyethylene glycol;    -   R³ and R⁴ are independently hydrogen; hydroxyl; —OR⁵; —NH₂;        —NHR⁶; —NR⁷R⁸, C₁₋₂₀ alkyl; C₁₋₂₀ alkyl sulfonate, C₁₋₂₀ alkyl        carboxylic acid or carboxylate; C₁₋₂₀ alkyl amino or quaternized        amino; —COOH; —CO₂ ⁻; or —SO₃ ⁻; wherein R⁵-R⁸ are independent        selected from the group consisting of C₁₋₂₀ alkyl or aryl;        oligoethylene glycol, or polyethylene glycol;    -   Z is carbon, nitrogen, sulfur, or oxygen, wherein if Y and/or Z        is carbon, the carbon is tetravalent having two substituents as        defined above; if Y and/or Z is sulfur and/or oxygen; the sulfur        and/or oxygen is divalent; and if Y and/or Z is nitrogen, the        nitrogen is trivalent, having one substituent as defined above;    -   R¹² is H or D; and    -   the benzene ring represented by dotted lines is optional.

G. Compounds of Formula VII

Hydrocyanine and deuterocyanine dyes as described in InternationalPatent Publication No. WO 2012/061403 can be used in the methods of theinvention. In some embodiments, for example, the hydro/deteurocyaninedye is a compound according to formula VII:

-   wherein Y represents the atoms necessary to form one to two fused    aromatic rings having 6 atoms in each ring, wherein the Y atoms are    selected from the group consisting of —CH, —C, —CR¹, and —N(R²)_(β),    where β is 0 or 1, but no more than one of the atoms in Y is    —N(R²)_(β), and each R¹ is independently amino, sulfo,    trifluoromethyl, hydroxyl, halogen, carboxy, C₁-C₆ alkyl, C₁-C₆    alkoxy, C₁-C₆ alkylamino, or C₂-C₁₂ dialkylamino, wherein each alkyl    portion of which is optionally substituted with substituents    selected from the group consisting of carboxy, sulfo, amino, and    hydroxy;    -   α is 1, and α+β=1 or 2;    -   W represents the atoms necessary to form one to two fused        aromatic rings having 6 atoms in each ring, wherein the W atoms        are selected from the group consisting of —CH, —C, —CR¹, and        —N(R¹²)_(β′), where β′ is 0 or 1, but no more than one of the        atoms in W is —N(R¹²)_(β′), and each R^(1′) is independently        amino, sulfo, trifluoromethyl, hydroxyl, halogen, carboxy, C₁-C₆        alkyl, C₁-C₆ alkoxy, C₁-C₆ alkylamino, or C₂-C₁₂ dialkylamino,        wherein each alkyl portion of which is optionally substituted        with substituents selected from the group consisting of carboxy,        sulfo, amino, and hydroxy;    -   δ is 1, and δ+β′⁼1 or 2;    -   R² and R¹² are independently L-Y—Z, an ionic group,        alkoxycarbonylalkyl, alkoxythiocarbonylalkyl,        thioalkoxycarbonylalkyl, alkenoxycarbonylalkyl,        alkenoxythiocarbonylalkyl, thioalkenoxycarbonylalkyl,        alkoxycarbonylalkenyl, alkoxycarbonylalkenyl,        thioalkoxycarbonylalkenyl, each alkyl or alkenyl portion of        which is C₁-C₂₂ alkyl or alkenyl that optionally incorporates up        to six hetero atoms, selected from N, O and S, and each alkyl        portion of which is optionally substituted one or more times        with F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate, amino,        sulfate, phosphonate, cyano, nitro, azido, C₁-C₆ alkoxy, C₁-C₆        alkylamino, C₂-C₁₂ dialkylamino, or C₃-C₁₈ trialkylammonium;    -   X is O, S, Se, —CR³R⁴, or —NR⁵, wherein        -   R³ and R⁴ are independently C₁-C₂₂ alkyl or C₇-C₂₂            arylalkyl, each alkyl portion of which optionally            incorporates up to six hetero atoms, selected from N, O and            S, and each alkyl portion of which is optionally substituted            one or more times with F, Cl, Br, I, hydroxy, carboxy,            sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro,            azido, C₁-C₆ alkoxy, C₁-C₆ alkylamino, or C₂-C₁₂            dialkylamino, or C₃-C₁₈ trialkylammonium; or R³ and R⁴ taken            in combination complete a five- or six-membered saturated or            unsaturated ring that is optionally substituted with F, Cl,            Br, I, hydroxy, carboxy, sulfo, phosphate, amino, sulfate,            phosphonate, cyano, nitro, azido, C₁-C₆ alkoxy, C₁-C₆            alkylamino, or C₂-C₁₂ dialkylamino, or C₃-C₁₈            trialkylammonium; and        -   R⁵ is H or C₁-C₂₂ alkyl that is optionally substituted one            or more times with hydroxy, carboxy, sulfo, amino, C₁-C₆            alkylamino or C₂-C₁₂ dialkylamino;    -   Z is O, S, Se, —CR¹³R¹⁴, or —NR¹⁵, wherein        -   R¹³ and R¹⁴ are independently C₁-C₂₂ alkyl or C₇-C₂₂            arylalkyl, each alkyl portion of which optionally            incorporates up to six hetero atoms, selected from N, O and            S, and each alkyl portion of which is optionally substituted            one or more times with F, Cl, Br, I, hydroxy, carboxy,            sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro,            azido, C₁-C₆ alkoxy, C₁-C₆ alkylamino, or C₂-C₁₂            dialkylamino, or C₃-C₁₈ trialkylammonium; or R¹³ and R¹⁴            taken in combination complete a five- or six-membered            saturated or unsaturated ring that is optionally substituted            with F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate,            amino, sulfate, phosphonate, cyano, nitro, azido, C₁-C₆            alkoxy, C₁-C₆ alkylamino, or C₂-C₁₂ dialkylamino, or C₃-C₁₈            trialkylammonium; and        -   R¹⁵ is H or C₁-C₂₂ alkyl that is optionally substituted one            or more times with hydroxy, carboxy, sulfo, amino, C₁-C₆            alkylamino or C₂-C₁₂ dialkylamino;    -   each of R²¹, R²², R²³ is independently H, F, Cl, C₁-C₆ alkyl,        C₁-C₆ alkoxy, aryl, aryloxy, a nitrogen heterocycle, an iminium        ion; or any two adjacent substituents of R²¹, R²², R²³, when        taken in combination, forms an aryl group or a 4-, 5-, or        6-membered saturated or unsaturated hydrocarbon ring that is        optionally substituted one or more times with C₁-C₆ alkyl,        halogen, or a carbonyl oxygen; or R²¹ taken in combination with        one of R³ and R⁴ forms a six-membered ring that is optionally        substituted with C₁-C₆ alkyl; or R²³ adjacent to Z, taken in        combination with one of R¹³ and R¹⁴ forms a six-membered ring        that is optionally substituted by a C₁-C₆ alkyl;    -   R²⁴ is H or D in either R or S configuration;    -   n is 0, 1, 2, or 3;    -   L is an optional member selected from the group of a bond, a        C₁-C₁₀ alkylene, and a C₁-C₁₀ alkenylene; wherein the alkylene        or alkenylene is optionally interrupted by at least one        heteroatom;    -   Y is an optional member selected from the group of a bond, —O—,        —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR^(15′)—, —NR^(15′)C(O)—,        —C(O)NR^(15′)—, —NZ—, —NZC(O)—, and —C(O)NZ—;    -   each Z is an independently selected C₁-C₁₀ alkyl that is        additionally substituted with one member from the group of        R^(13′) and R^(16′);    -   each R^(13′) is a member independently selected from the group        of hydroxyl, amino, carboxyl, alkoxycarbonyl, amido, sulfonato,        and thioacetyl;    -   R^(15′) is a member selected from the group of alkyl and        alkoxycarbonylalkyl; wherein the alkyl is optionally interrupted        by at least one heteroatom; and    -   each R^(16′) is independently a member selected from the group        of activated acyl, formyl, glycidyl, halo, haloalkyl,        hydrazidyl, isothiocyanato, iodoacetamidyl, maleimidyl,        mercapto, phosphoramidityl, and vinyl sulfonyl. In a preferred        aspect, R^(16′) is activated acyl, maleimidyl, phosphoramidityl,        or glycidyl.

In a preferred aspect, L is not present. Alternatively, L is a C₁-C₁₀alkylene interrupted by ether linkages (e.g., a polyethylene glycololigomer).

In a preferred aspect, Y is a bond. Alternatively, Y is —O—.Alternatively, Y is an amido group optionally substituted with R^(15′)at the amido nitrogen.

In a more preferred aspect, Z is C₁-C₆ alkyl. Alternatively, Z isinterrupted by ether linkages (e.g., a polyethylene glycol oligomer). Ina still more preferred aspect, Z is carboxyalkyl or sulfonatoalkyl. In ayet still more preferred aspect, Z is 5-carboxypentyl or 4-carboxybutyl.

In another alternative preferred aspect, -L-Y— is a bond; Z is(CH₂)_(t)R^(13′); R^(13′) is carboxyl or activated acyl; and t is aninteger from 1 to 10 such as 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.Alternatively, t is an integer from 0 to 10.

In still another alternative preferred aspect, the Z group's L group isa bond. Alternatively, Z is R^(13′) or R^(16′) that is directly bondedto the phenyl ring itself if L and Y are also bonds.

In yet still another alternative preferred aspect, -L-Y—Z has at leastfour carbons. Alternatively, Z has at least four carbons.

In a preferred embodiment, R^(13′) is carboxyl, amido, oralkoxycarbonyl. In a more preferred embodiment, R^(13′) is carboxyl.Alternatively, R^(13′) is sulfonato.

In a preferred aspect, R^(15′) is alkyl. In a more preferred aspect, R¹⁵is lower alkyl. Alternatively, R^(15′) is interrupted by ether linkages(e.g., a polyethylene glycol oligomer).

In a preferred aspect, R^(16′) is activated acyl, maleimidyl,phosphoramidityl, or glycidyl. In a more preferred embodiment, R^(16′)is activated acyl. Alternatively, R^(16′) is activated ester. In a stillmore preferred embodiment, R^(16′) is succinimidyloxy-ester orsulfosuccinimidyloxy-ester.

Some embodiments of the invention provide methods where in thehydro/deteurocyanine dye is selected from the compounds in Table 1.

TABLE 1 Hydrocyanine and Deuterocyanine Dyes for ROS Imaging andImmunoassays Compound No. Compound Name Compound Structure 1 H-IR650DIOL

2 H-IR680DIOL

3 H-IR675

4 H-IR780F2

5 H-IRDye ® 800CW

6 H-Cy5

7 H-Cy3

III. Methods of Making

Many of the cyanine dyes (oxidized form) used to make the compounds ofFormula I-VII (reduced dye) are commercially available from LI-CORBiosciences, Lincoln Nebr. As used herein, “reduced dye” includes a dyemolecule in which one or more t-bonds have been reduced, disrupting theextended π-conjugation, resulting in a molecule that exhibits negligibleor no fluorescence. For example, “reduced cyanine dye,” “hydrocyanine,”or “deuterocyanine” include a cyanine dye wherein the iminium cation hasbeen reduced to make a compound of the present invention.“Deuterocyanine,” as used herein, includes a cyanine dye that has beenreduced by a deuterated reducing agent thus incorporating deuterium intothe reduced molecule.

For example, with reference to FIG. 7, to a solution of IRDye® 800CWcarboxylate, commercially available from LI-COR Biosciences, sodiumborohydride was added. The reaction mixture was stirred at roomtemperature for 15 minutes. After chromatography, the reduced dye wasisolated.

Certain of the compounds of Formula I in their oxidized form aredisclosed in WO 2012/054784, the teachings of which are herebyincorporated by reference in its entirety for all purposes. In oneaspect, the oxidized form of the cyanine compounds scan be preparedusing a procedure for a Schiff base such as the one included in U.S.Pat. No. 6,747,159 (Ar=Ph; pyridine/Ac₂O, Δ). The substituent canoptionally be modified after the synthesis of the polymethine bridge(e.g., deprotected, activated for reaction with a biomolecule, orreacted to form a linking group).

In another aspect, the oxidized cyanine compounds of Formula I areprepared by means of an organometallic coupling to incorporate asubstituent to the polymethine bridge. More preferably, the substituentis installed by means of a palladium coupling. The substituent canoptionally be modified after its inclusion (e.g., deprotected, activatedfor reaction with a biomolecule, or reacted to form a linking group).Subsequent reduction yields the compounds of Formula I.

Certain of the compounds of Formula II in their oxidized form aredisclosed in U.S. Pat. No. 6,995,274, the teachings of which are herebyincorporated by reference in its entirety for all purposes. In general,substituted or unsubstituted indolesulfonate quaternary salts arereacted with a commercially available Schiffs base such asN-[(3-(anilinomethylene)-2-chloro-1-cyclohexen-1-yl) methylene]anilinemonohydrochloride using techniques and reaction conditions that are wellknown in the art. The product is then reacted with a hydroxybenzenesulfonic acid to give an oxidized dye. Subsequent reduction yields acompound of Formula II.

With respect to the compounds of Formula III, the oxidized form of thecyanine dyes are disclosed in WO 2010/121163, the disclosure of which ishereby incorporated by reference in its entirety for all purposes. Inbrief, the oxidized compounds of Formula I are prepared by reaction witha dialdehyde or dialdehyde equivalent (e.g., a Schiff base) that alreadyincorporates the substituent for the polymethine bridge. Arepresentative procedure for a dialdehyde is included in pending U.S.patent application Ser. No. 12/065,391 (US 2008/0267883 A1). Arepresentative procedure for a Schiff base is included in U.S. Pat. No.6,747,159 (Ar=Ph; pyridine/Ac₂O, Δ). The substituent can optionally bemodified after the synthesis of the polymethine bridge (e.g.,deprotected, activated for reaction with a biomolecule, or reacted toform a linking group).

In another aspect, the oxidized cyanine compounds of Formula III areprepared by means of an organometallic coupling to incorporate asubstituent to the polymethine bridge. More preferably, the substituentis installed by means of a palladium coupling. The substituent canoptionally be modified after its inclusion (e.g., deprotected, activatedfor reaction with a biomolecule, or reacted to form a linking group).Subsequent reduction yields the compounds of Formula III.

With respect to the compounds of Formula IV, the oxidized form of thecyanine dyes are disclosed in WO 2012/054749, the disclosure of which ishereby incorporated by reference in its entirety for all purposes. Inbrief, the cyanine compounds set forth in Formula II are prepared bymeans of an organometallic coupling to incorporate a substituent to thepolymethine bridge. More preferably, the substituent is installed bymeans of a palladium coupling. The substituent can optionally bemodified after its inclusion (e.g., deprotected, activated for reactionwith a biomolecule, or reacted to form a linking group). In certaininstances, the polymethine substrate for the Suzuki coupling is a3-halopentamethine. In a preferred embodiment, the halo-substituent is achloride or a bromide.

Certain of the compounds of Formula V are prepared using a procedure asset forth in Example 13.

Hydrocyanine and deuterocyanine dyes of Formula VI are as described inU.S. Patent Application Publication No. 2011/0070166, incorporatedherein by reference in its entirety. Hydrocyanine and deuterocyaninedyes of Formula VII are as described in WO 2012/061403, incorporatedherein by reference in its entirety.

IV. Methods of Labeling Biomolecules or Conjugates

The compounds of Formula I-VII can be attached to biomolecules or otherdyes. Methods of linking dyes to various types of biomolecules arewell-known in the art. For a thorough review of, e.g., oligonucleotidelabeling procedures, see R. Haugland in Excited States of Biopolymers,Steiner ed., Plenum Press (1983), Fluorogenic Probe Design andSynthesis: A Technical Guide, PE Applied Biosystems (1996), and G. T.Herman, Bioconjugate Techniques, Academic Press (1996).

“Click” chemistry provides one possible way for linking the inventivedyes to biomolecules. Click chemistry uses simple, robust reactions,such as the copper-catalyzed cycloaddition of azides and alkynes, tocreate intermolecular linkages. For a review of click chemistry, seeKolb, H. C.; Finn, M. G.; Sharpless, K. B. Angew. Chem. 2001, 40, 2004.

Connection (or ligation) of two fragments to make a larger molecule orstructure is often achieved with the help of so-called “click chemistry”described by Sharpless et al. Angew. Chem, Int. Ed. 40: 2004 (2001).This term is used to describe a set of bimolecular reactions between twodifferent reactants such as azides and acetylenes. The formation of1,2,3-triazoles in 1,3-dipolar cycloaddition of azides to a triple bondis known, but because the activation energy of acetylene-azidecycloaddition is relatively high, the reaction is slow under ambientconditions.

The utility of the reaction of azides with alkynes was expanded by thediscovery of Cu (I) catalysis. 1,3-cycloaddition of azides to terminalacetylenes in the presence of catalytic amounts of cuprous salts isfacile at room temperature in organic or aqueous solutions.

U.S. Pat. No. 7,807,619 to Bertozzi et al. teaches modified cycloalkynecompounds and method of use of such compounds in modifying biomolecules.Bertozzi et al. teach a cycloaddition reaction that can be carried outunder physiological conditions. As disclosed therein, a modifiedcycloalkyne is reacted with an azide moiety on a target biomolecule,generating a covalently modified biomolecule.

The present invention provides reduced cyanine dyes with click chemistryfunctionalities useful for labeling biomolecules. As such, in oneaspect, the present invention provides compounds of Formula I-VII, inwhich in one embodiment, each R¹⁶ is independently a member selectedfrom the group consisting of activated acyl, acrylamido, optionallysubstituted alkylsulfonate ester, azido, optionally substitutedarylsulfonate ester, amino, azido, aziridino, boronato, diazo, formyl,glycidyl, halo, haloacetamidyl, haloalkyl, haloplatinato, halotriazino,hydrazinyl, imido ester, isocyanato, isothiocyanato, maleimidyl,mercapto, phosphoramidityl, a photoactivatable moiety, vinyl sulfonyl,alkynyl, a pegylated azido group, and a pegylated alkynyl group; and inwhich at least one R¹⁶ is independently a member selected from the groupazido, alkynyl, a pegylated azido and a pegylated alkynyl.

In yet other aspects, the present invention relates to two componentsthat interact with each other to form a stable covalent bio-orthogonalbond. Bio-orthogonal reactions are reactions of materials with eachother, wherein each material has limited or essentially no reactivitywith functional groups found in vivo. These components are of use inchemical and biological assays, as chemical reagents, medical imagingand therapy, and more particularly, in nucleic acid modificationtechniques. According to a particular embodiment of the invention, thecovalent bio-orthogonal bond is obtained by the [3+2] cycloaddition ofazides and alkynes.

In still other aspects, one of the two components that interact witheach other to form a stable covalent bio-orthogonal bond is a nearinfrared dye, such as a reduced cyanine dye. In a preferred aspect, thereduced cyanine dyes of the present invention comprise either an azideor an alkyne group for use as a reactant in a click chemistry reactionand the other reactant is a biomolecule such as a nucleotide comprisingeither an alkyne or azide group.

Azide reactive groups such as an alkyne compounds can react with atleast one 1,3-dipole-functional compound such as an alkyne reactivegroup (e.g., a azido group) in a cyclization reaction to form aheterocyclic compound. In certain embodiments, the reaction can becarried out in the presence of an added catalyst (e.g., Cu(I)). In otherembodiments, the reaction is carried out in the absence of suchcatalysts. Exemplary 1,3-dipole-functional compounds include, but arenot limited to, azide-functional compounds, nitrile oxide-functionalcompounds, nitrone-functional compounds, azoxy-functional compounds,and/or acyl diazo-functional compounds. Preferably, azide-functionalcompounds are used.

Suitable biomolecule moieties for click reaction include, for example,monomeric and polymeric derivatives of nucleotides, carbohydrates, aminoacids, lipids, glycols, alkanes, alkenes, arene, silicates, as well asbiologically active and inactive compounds obtained from nature or fromartificial synthesis.

Other suitable biological molecules include those having a azido oralkynyl functionality, which include, but are not limited to, anantibody, an antigen, an avidin, a carbohydrate, a deoxy nucleic acid, adideoxy nucleotide triphosphate, an enzyme cofactor, an enzymesubstrate, a fragment of DNA, a fragment of RNA, a hapten, a hormone, anucleic acid, a nucleotide, a nucleotide triphosphate, a nucleotidephosphate, a nucleotide polyphosphate, an oligosaccharide, a peptide,PNA, a polysaccharide, a protein, a streptavidin, and the like. Thesebiological molecules will in turn be reacted with the dye compounds ofthe present invention comprising either an azide or an alkyne group foruse in click chemistry reactions.

In one aspect, the reduced cyanine compounds of Formula I-VII havesufficient solubility in aqueous solutions that once they are conjugatedto a soluble ligand or biomolecule, the ligand or biomolecule retainsits solubility. In certain instances, the bioconjugates also have goodsolubility in organic media (e.g., DMSO or DMF), which providesconsiderable versatility in synthetic approaches to the labeling ofdesired materials.

In another aspect, the present invention provides a method or processfor labeling a ligand or biomolecule with a compound of Formula I-VII,the method comprising: contacting a ligand or biomolecule with acompound having Formula I-VII to generate the correspondingbioconjugate.

In one preferred embodiment, the R¹⁶ group or the R¹³ group reacts witha thiol, a hydroxyl, a carboxyl, or an amino group on a biomolecule,forming a linking group between the dye and the biomolecule. In a morepreferred embodiment, this reaction is carried out in mixtures ofaqueous buffer and an organic solvent such as DMF at pH 8 to 9.Alternatively, this reaction is carried out in distilled water or in anaqueous buffer solution. For thiols or for acidic groups, a pH of 7 orlower is preferred for the reaction solvent, especially if a substratealso contains a reactive amino group.

Selected examples of reactive functionalities useful for attaching acompound of Formula I-VII to a ligand or biomolecule are shown in Table2, wherein the bond results from the reaction of a dye with a ligand orbiomolecule. Column A of Table 2 is a list of the reactivefunctionalities, which can be on the compound of Formula I-VII or thebiomolecule. Column B is a list of the complementary reactive groups(preferably, a carboxyl, hydroxyl, thiol, or amino functionality), whichcan be on the biomolecule or the compound of Formula I-VII, and whichreact with the indicated functionality of Column A to form the bond ofColumn C. Those of skill in the art will know of other bonds suitablefor use in the present invention.

TABLE 2 Exemplary Bonds for Linking Groups B A Complementary C ReactiveFunctionality Group (Biomolecule Resulting (Compound of Formula orCompound Linking I-VII or Biomolecule) of Formula I-VII) Group activatedesters* amines/anilines amides acrylamides thiols thioethers acylazides** amines/anilines amides acyl halides amines/anilines amides acylhalides alcohols/phenols esters acyl nitriles alcohols/phenols estersacyl nitriles amines/anilines amides aldehydes amines/anilines iminesaldehydes or ketones hydrazines hydrazones aldehydes or ketoneshydroxylamines oximes alkyl halides amines/anilines alkyl amines alkylhalides carboxylic acids esters alkyl halides thiols thioethers alkylhalides alcohols/phenols ethers anhydrides alcohols/phenols estersanhydrides amines/anilines amides/imides aryl halides thiols thiophenolsaryl halides amines aryl amines azides alkynes 1,2,3-triazoles azidesester with phosphine amide (and phosphine reagent (e.g., o- oxide)diphenylphosphino group) aziridines thiols thioethers boronates glycolsboronate esters boronates/boronic acids aryl halides C-C bond to arylring boronates/boronic acids alkenyl halides C-C bond to alkenyl groupactivated carboxylic acids amines/anilines amides activated carboxylicacids alcohols esters activated carboxylic acids hydrazines hydrazidescarbodiimides carboxylic acids N-acylureas or anhydrides diazoalkanescarboxylic acids esters electron-rich diene dienophile (e.g.,cyclohexene (Diels- electron-poor Alder cycloaddition) alkene) epoxidesthiols thioethers epoxides amines alkyl amines epoxides carboxylic acidsesters haloacetamides thiols thioethers haloplatinate amino platinumcomplex haloplatinate heterocycle platinum complex halotriazinesamines/anilines aminotriazines halotriazines alcohols/phenols triazinylethers imido esters amines/anilines amidines isocyanates amines/anilinesureas isocyanates alcohols/phenols urethanes isothiocyanatesamines/anilines thioureas maleimides thiols thioethers phosphoramiditesalcohols phosphite esters photoactivatable group varies; see definitionvaries; see definition quadricyclanes π-electrophile (e.g., norborneneNi bis(dithiolene)) cycloaddition product silyl halides alcohols silylethers sulfonyl azides thiocarboxylic acids N-acyl sulfonamidessulfonate esters amines/anilines alkyl amines sulfonate esterscarboxylic acids esters sulfonate esters thiols thioethers sulfonateesters alcohols/phenols ethers sulfonyl halides amines/anilinessulfonamides 1,2,4,5-tetrazine alkene dihydropyradazine vinyl sulfonylthiols thioethers vinyl sulfonyl activated diene cyclohexenyl (Diels-Alder) *Activated esters, as understood in the art, generally have theformula —C(O)OM, where —OM is a leaving group (e.g. succinimidyloxy(—OC₄H₄NO₂), sulfosuccinimidyloxy (—OC₄H₃NO₂SO₃H), -1-oxybenzotriazolyl(—OC₆H₄N₃); 4-sulfo-2,3,5,6-tetrafluorophenyl; or an aryloxy group oraryloxy substituted one or more times by electron withdrawingsubstituents such as nitro, fluoro, chloro, cyano, or trifluoromethyl,or combinations thereof, used to form activated aryl esters; or —C(O)OMis a carboxylic acid activated by a carbodiimide to form an anhydride ormixed anhydride —C(O)OC(O)R^(a) or —C(O)OC(NR^(a))NHR^(b), wherein R^(a)and R^(b) are members independently selected from the group consistingof C₁-C₆ alkyl, C₁-C₆ perfluoroalkyl, C₁-C₆ alkoxy, cyclohexyl,3-dimethylaminopropyl, or N-morpholinoethyl). **Acyl azides can alsorearrange to isocyanates.

Some methods of forming linking groups include those taught in Slettenand Bertozzi, J. Am. Chem. Soc. electronic publication atdx.doi.org/10.1021/ja2072934; Devaraj and Weissleder, Acc. Chem. Res.electronic publication at dx.doi.org/10.1021/ar200037t; Krishnamoorthyand Begley, J. Am. Chem. Soc. electronic publication atdx.doi.org/10.1021/ja1034107; and the like.

When linking a compound of Formula I-VII having a carboxylic acid withan amine-containing ligand or biomolecule, the carboxylic acid can firstbe converted to a more reactive form, e.g, a N-hydroxy succinimide (NHS)ester or a mixed anhydride, by means of an activating reagent. Theamine-containing ligand or biomolecule is treated with the resultingactivated acyl to form an amide linkage. In a more preferred embodiment,this reaction is carried out in aqueous buffer at pH 8 to 9 with DMSO orDMF as an optional co-solvent. Alternatively, this reaction is carriedout in distilled water or in an aqueous buffer solution.

Similarly, the attachment of an isocyanate- or isothiocyanate-containingcompound of Formula I-VII is analogous to the procedure for the carboxydye, but no activation step is required. The amine-containing ligand orbiomolecule is treated directly with the activated acyl compound to forma urea or a thiourea linkage. In a more preferred embodiment, thereaction is carried out in aqueous buffer at pH 9 to 10 with DMSO or DMFas an optional co-solvent. Alternatively, this reaction is carried outin distilled water or in an aqueous buffer solution.

If the compound of Formula I-VII or biomolecule has a reactive hydroxylgroup, it can be linked to a ligand or biomolecule by means ofphosphoramidite chemistry, which ultimately forms a phosphate linkagebetween the dye and the biomolecule. For examples of such labelingmethods, see U.S. Pat. No. 6,027,709, which discloses many preferredlinking groups, linking methods, and biomolecules that can be readilylabeled. In one embodiment, solid-phase synthesis is preferred, asdisclosed in U.S. Pat. No. 6,027,709.

In a preferred embodiment, the biomolecule is DNA or RNA. Use ofphosphoramidite chemistry allows labeling of a DNA or an RNA during thesynthesis process. The protected nucleotide is labeled while attached toa solid-phase support. The free 5′-OH group is reacted with thephosphoramidite and a tetrazole activator to form a phosphite linkagewhich subsequently is oxidized to phosphate. The labeled DNA or RNA isthen cleaved from the solid phase by means of ammonia or by anotherstandard procedure.

It is generally preferred to prepare a phosphoramidite of a reducedcyanine dye to label DNA molecules in a DNA synthesizer. It is alsopreferred to attach the dye to the 5′ end of a protected, support-bondedoligonucleotide through standard phosphoramidite chemistry. For a listof preferred label terminators for use in DNA sequencing, see U.S. Pat.No. 5,332,666.

In another preferred embodiment, the biomolecule is an antibody. It ispreferred that antibody labeling is carried out in a buffer optionallyincluding an organic co-solvent, under basic pH conditions, and at roomtemperature. It is also preferred that the labeled antibody be purifiedby dialysis or by gel permeation chromatography using equipment such asa SEPHADEX® G-50 column to remove any unconjugated compound of FormulaI-VII. Those of skill in the art will know of other ways and means forpurification.

In still another preferred embodiment, the biomolecule contains a thiolgroup that forms the linking group by reaction with a maleimidylsubstituent at R¹⁶. In a more preferred embodiment, the biomolecule is aprotein, a peptide, an antibody, a thiolated nucleotide, or a thiolateddeoxynucleotide.

In yet other aspects, the linking group or biomolecule comprises apolymer. In a preferred embodiment, the polymer is a member selectedfrom the group of a PEG, a copolymer of PEG-polyurethane, and acopolymer of PEG-polypropylene. In still yet other aspects, the linkinggroup is a member selected from the group of a polysaccharide, apolypeptide, an oligosaccharide, a polymer, a co-polymer and anoligonucleotide.

In one aspect, biomolecules can be labeled according to the presentinvention by means of a kit. In certain instances, the kit comprises abuffer and a dye as disclosed in the instant application (e.g., acompound of Formula I). Preferably, the kit contains a coupling buffersuch as 1 M KH₂PO₄ (pH 5), optionally with added acid or base to modifythe pH (e.g., pH 8.5 is preferred for reactions with succinimide estersand pH 7 is preferred for reactions with maleimides). Preferably, thebuffer has a qualified low fluorescence background.

Optionally, the kit can contain a purification sub-kit. After labeling abiomolecule with a preferred dye, the labeled biomolecule may beseparated from any side reaction products and any free hydrolyzedproduct resulting from normal hydrolysis. For biomolecules containing 13or fewer amino acids, preparative thin layer chromatography (TLC) canremove impurities. In certain instances, preparative TLC, optionallyperformed with commercially available TLC kits, can be used to purifydye-labeled peptides or proteins.

For larger biomolecules such as larger peptides or proteins, a SEPHADEX®G-15, G-25, or G-50 resin may remove unwanted derivatives. In certaininstances, a Gel Filtration of Proteins Kit, which is commerciallyavailable from Life Sciences, can be used to separate dye-labeledpeptides and proteins from free dye. The labeled biomolecules thatremain after desalting can often be used successfully without furtherpurification. In some cases, it may be necessary to resolve and assessthe activity of the different products by means of HPLC or otherchromatographic techniques.

V. Conjugate Compounds

A. Bioconjugates

In another embodiment of the invention, bioconjugates are providedwherein a compound of Formula I, II, III, IV, V, VI, or VII is reactedwith a biomolecule to generate a conjugate of Formula I^(L), II^(L),III^(L), IV^(L), V^(L), VI^(L) or VII^(L), respectively.

Each Z of Formula I, II, III, IV, V, VI, or VII becomes Z^(L) in FormulaI^(L), II^(L), III^(L), IV^(L), V^(L), VI^(L) or VII^(L), wherein Z^(L)is an independently selected C₁-C₁₀ alkyl that is additionallysubstituted with one member from the group of R¹³ or R^(L). In a morepreferred aspect, Z^(L) is C₁-C₆ alkyl. Alternatively, Z^(L) isinterrupted by ether linkages (e.g., a polyethylene glycol oligomer). Ina yet still more preferred aspect, at least one Z^(L) is-propylene-C(O)—R^(L) or -butylene-C(O)—R^(L). Alternatively, exactlyone Z^(L) is -propylene-C(O)—R^(L) or -butylene-C(O)—R^(L).

In an alternative aspect, Z^(L) is optional, and R^(L) is connecteddirectly to -L-Y— or even directly bonded to a portion of the reduceddye itself if L and Y are absent.

Each R^(L) (e.g., R^(L) as disclosed previously in the specification)comprises 1) a linking group that connects the reduced cyanine dyecompound to a biomolecule; and 2) the biomolecule to which it isconnected (i.e., the linking group and the biomolecule connectedthereby). In a preferred embodiment, a bioconjugate compound comprisesat least one R^(L) Preferred linking groups are indicated in Table 2(column C). In a particularly preferred aspect, the linking group is anamide or an ester. In a more particularly preferred aspect, the linkinggroup is an amide.

The compound has a balanced charge. In a preferred aspect, thecompound's net anionic charge is balanced by alkali metal counterions(e.g., sodium or potassium). In a more preferred aspect, at least one ofthe counterions is sodium. Alternatively, all of the counterions aresodium.

In another preferred embodiment of the bioconjugate, any preferredembodiments or aspects of the inventive compound of Formula I-VII canincluded in the embodiment of a bioconjugate of Formula I^(L), II^(L),III^(L), IV^(L), V^(L), VI^(L) or VII^(L).

In certain aspects, preferred biomolecules for the instant inventioninclude an acyclo terminator triphosphate, an antibody, an antigen, anavidin, a carbohydrate, a deoxy nucleic acid, a dideoxy nucleotidetriphosphate, an enzyme cofactor, an enzyme substrate, a fragment ofDNA, a fragment of RNA, a hapten, a hormone, a nucleic acid, anucleotide, a nucleotide triphosphate, a nucleotide phosphate, anucleotide polyphosphate, an oligosaccharide, a peptide, PNA, apolysaccharide, a protein, a streptavidin, and the like.

In still other instances, suitable nucleotides include nucleosidepolyphosphates, including, but not limited to, deoxyribonucleosidepolyphosphates, ribonucleoside polyphosphates, dideoxynucleosidepolyphosphates, carbocyclic nucleoside polyphosphates and acyclicnucleoside polyphosphates and analogs thereof. Nucleotides containing 3,4, 5, 6, or more phosphate groups, in the polyphosphate chain, where thephosphate (e.g., α, β, γ, ε, or terminal phosphate), sugar, base, orcombination thereof is labeled with a compound of Formula I-VII. Thepolyphosphate nuceotides include, but are not limited to,tetraphosphates, pentaphosphates, hexaphosphates, heptaphosphates, andthe like. The bases include for example, purines, (adenine and guanine)pyrimidines, (thymine, uracil and cytosine) and derivatives thereof.

In certain instances, the dye of Formula I is attached to the phosphate(e.g. α, β, γ, ε-phosphate or terminal phosphate) through aphosphorothioate linkage (see, for example, U.S. Pat. No. 6,323,186,incorporated herein by reference), heteroatom, or functional group A, orB, resulting in linkage C of Table I. See also U.S. Pat. No. 6,399,335(incorporated herein by reference) entitled “γ-phosphoester nucleosidetriphosphates,” which provides methods and compositions for polymerizingparticular nucleotides with a polymerase using γ-phosphoester linkednucleoside triphosphates. Other ways of linking the compounds of FormulaI to a nucleotide are known to those of skill in the art. Using thesenucleotides with a DNA polymerase can lead to identification of specificnucleotides in a DNA or RNA sequence by identification of the labeledpyrophosphate or polyphosphate released upon incorporation of thenucleotide base into RNA or DNA. (See for example, U.S. Pat. No.6,232,075, U.S. Pat. Publ. No. 2004/0241716 and U.S. Pat. No. 7,452,698each of which is incorporated herein by reference).

More preferred aspects include an antibody, an avidin, and astreptavidin. Even more preferred aspects include a goat anti-mouse(GAM) antibody, a goat anti-rabbit (GAR) antibody, and streptavidin.

In certain other aspects, preferred biomolecules for the instantinvention include somatostatin, endostatin, a carbohydrate, anoligosaccharide, an aptamer, a liposome, PEG, an angiopoietin,angiostatin, angiotensin II, α₂-antiplasmin, annexin V, β-cyclodextrintetradecasulfate, endoglin, endosialin, endostatin, epidermal growthfactor, fibrin, fibrinopeptide β, fibroblast growth factor, FGF-3, basicfibronectin, fumagillin, heparin, hepatocycte growth factor, hyaluronan,aninsulin-like growth factor, an interferon-α, β inhibitor, ILinhibitor, laminin, leukemia inhibitory factor, linomide, ametalloproteinase, a metalloproteinase inhibitor, an antibody, anantibody fragment, an acyclic RGD peptide, a cyclic RGD peptide,placental growth factor, placental proliferin-related protein,plasminogen, plasminogen activator, plasminogen activator inhibitor-1, aplatelet activating factor antagonist, platelet-derived growth factor, aplatelet-derived growth factor receptor, a platelet-derived growthfactor receptor, platelet-derived endothelial cell growth factor,pleiotropin, proliferin, proliferin-related protein, a selectin, SPARC,a snake venom, substance P, suramin, a tissue inhibitor of ametalloproteinase, thalidomide, thrombin, thrombin-receptor-activatingtetradecapeptide, transformin growth factor-α, β, transforming growthfactor receptor, tumor growth factor-α, tumor necrosis factor,vitronectin, and the like.

In still other aspects, preferred biomolecules include a carbohydrateand a carbohydrate derivative. Representative examples includeglucosamine, a glyceraldehyde, erythrose, threose, ribose, arabinose,xylose, lyxose, allose, altrose, glucose, mannose, gulose, idose,galactose, talose, erythrulose, ribulose, xylulose, psicose, fructose,sorbose, tagatose, and a derivative thereof. Even more preferredbiomolecules include 2-deoxy-D-glucose, 2-deoxy-L-glucose, and racemic2-deoxyglucose.

In yet still other aspects, the biomolecule can be a ligand that hasaffinity for a receptor selected from the group of EGFR, Her2, PDGFR,IGFR, c-Ryk, c-Kit, CD24, integrins, FGFR, KFGR, VEGFR, TRAIL decoyreceptors, retinoid receptor, growth receptor, PPAR, vitamin receptor,glucocordicosteroid receptor, Retinoid-X receptor, RHAMM, high affinityfolate receptors, Met receptor, estrogen receptor and Ki67.

Alternatively, the biomolecule is selected from the group ofsomatostatin, endostatin, a carbohydrate, a monosaccaride, adisaccharide, a trisaccharide, an oligosaccharide, aptamer, liposome andpolyethylene glycol.

In yet another aspect, the biomolecule is a small-molecule drug ordrug-like molecule such as a tetracycline antibiotic, a tetracyclinederivative, and calcein. Other conjugates include pluonic nanocarriersfor example, see Ja-Young Kim et al., Journal of Controlled Release 156(2011) 398-405, incorporated herein by reference.

B. Ratiometric Probes

In yet another embodiment, the present invention provides ratiometricprobes. In this aspect, the reduced dyes of Formula I-VII can beconjugated using the techniques of Table 2 to another dye, preferably,an always on dye. Each R^(L) comprises 1) a linking group that connectsthe reduced cyanine dye compound to a dye; and 2) the dye to which it isconnected (i.e., the linking group and the dye connected thereby),wherein the compound comprises at least one R^(L). Preferred linkinggroups are indicated in Table 2 (column C). In a particularly preferredaspect, the linking group is an amide or an ester. In a moreparticularly preferred aspect, the linking group is an amide.

The ratiometric hydrocyanines are synthesized and tested in vitro byverifying that they possess sufficient cell permeability and ROSsensitivity to detect a quantitative increase of stimulated cells byexcitation of for example a BODIPY dye, and a hydrocyanine-660 dye at501 nm and 635 nm respectively. The intensity ratio of hydrocyanine-660emission at 660 nm upon reacting with ROS, to BODIPY Dye's emission at517 nm, 1660/1517, will show a ratiometric response toward ROS. In thecell culture studies, it is anticipated that a ratiometric responsetoward ROS from the Hydrocyanine-660 moiety with the BODIPY dye instimulated groups.

Exemplary fluorophores suitable for use in the present invention asratiometric probes include IRDye® 700DX, IRDye® 700, IRDye® 800RS,IRDye® 800CW, IRDye® 800, Cy5, Cy5.5, Cy7, DY 676, DY680, DY682, DY780,and mixtures thereof. Additional suitable fluorophores includeenzyme-cofactors; lanthanide, green fluorescent protein, yellowfluorescent protein, red fluorescent protein, or mutants and derivatesthereof. In one embodiment of the invention, the second member of thespecific binding pair has a detectable group attached thereto. Othersuitable dyes include those listed in the Molecular Probes Catalogue,which is herein incorporated by reference (see R. Haugland, TheHandbook—A Guide to Fluorescent Probes and Labeling Technologies,10^(th) Edition, Molecular probes, Inc. (2005)). Such exemplaryfluorophores include, but are not limited to, Alexa Fluor® dyes such asAlexa Fluor® 350, Alexa Fluor® 405, Alexa Fluor® 430, Alexa Fluor® 488,Alexa Fluor® 514, Alexa Fluor® 532, Alexa Fluor® 546, Alexa Fluor® 555,Alexa Fluor® 568, Alexa Fluor® 594, Alexa Fluor® 610, Alexa Fluor® 633,Alexa Fluor® 635, Alexa Fluor® 647, Alexa Fluor® 660, Alexa Fluor® 680,Alexa Fluor® 700, Alexa Fluor® 750, and/or Alexa Fluor® 790, as well asother fluorophores such as, for example, Dansyl Chloride (DNS-Cl),5-(iodoacetamida)fluoroscein (5-IAF), fluoroscein 5-isothiocyanate(FITC), tetramethylrhodamine 5- (and 6-)isothiocyanate (TRITC),6-acryloyl-2-dimethylaminonaphthalene (acrylodan),7-nitrobenzo-2-oxa-1,3,-diazol-4-yl chloride (NBD-Cl), ethidium bromide,Lucifer Yellow, 5-carboxyrhodamine 6G hydrochloride, Lissamine rhodamineB sulfonyl chloride, Texas Red™ sulfonyl chloride, BODIPY™,naphthalamine sulfonic acids (e.g., 1-anilinonaphthalene-8-sulfonic acid(ANS), 6-(p-toluidinyl)naphthalen-e-2-sulfonic acid (TNS), and thelike), Anthroyl fatty acid, DPH, Parinaric acid, TMA-DPH, Fluorenylfatty acid, fluorescein-phosphatidylethanolamine, TexasRed-phosphatidylethanolamine, Pyrenyl-phophatidylcholine,Fluorenyl-phosphotidylcholine, Merocyanine540,1-(3-sulfonatopropyl)-4-[β-[2[(di-n-butylamino)-6naphthyl]vinyl]pyridinium betaine (Naphtyl Styryl),3,3′dipropylthiadicarbocyanine (diS-C₃-(5)), 4-(p-dipentylaminostyryl)-1-methylpyridinium (di-5-ASP), Cy-3 Iodo Acetamide,Cy-5-N-Hydroxysuccinimide, Cy-7-Isothiocyanate, rhodamine 800, IR-125,Thiazole Orange, Azure B, Nile Blue, Al Phthalocyanine, Oxaxine 1, 4′,6-diamidino-2-phenylindole (DAPI), Hoechst 33342, TOTO, Acridine Orange,Ethidium Homodimer, N(ethoxycarbonylmethyl)-6-methoxyquinolinium (MQAE),Fura-2, Calcium Green, Carboxy SNARF-6, BAPTA, coumarin, phytofluors,Coronene, metal-ligand complexes,

Typically, the fluorescent group is a fluorophore selected from thecategory of dyes comprising polymethines, pthalocyanines, cyanines,xanthenes, fluorenes, rhodamines, coumarins, fluoresceins and BODIPY™.

Given the importance of ROS in physiology and pathology, the ratiometricprobes herein are useful for quantitative determination of ROS in cells,tissue and in vivo biomedical research. The ratiometric indicatorsdisclosed herein have significant advantages over single-emissionprobes. Measurements of ROS concentrations using fluorescence microscopyare sensitive to the effects of uneven dye loading, photobleaching,leakage of dye, and unequal cell thickness. The inventive ratiometricprobes afford simultaneous recording of two measurable signals in thepresence and absence of an analyte allow for accurate and quantitativereadouts.

VI. Methods of Imaging

In another embodiment, the compounds of Formula I-VII or theirbioconjugates can be used as in vitro or in vivo optical imaging agentsof tissues and organs in various biomedical applications. In oneembodiment, the present invention provides a method for imaging, themethod comprising administering a compound of Formula I-VII.

In certain preferred aspects of the invention, any of the embodiments oraspects of the inventive compound of Formula I-VII that are describedherein can be used in the method of imaging. Representative examples ofpreferred compounds for use in the method are described in thespecification and the dependent claims of the instant application.

In another embodiment, the present invention provides a method forimaging, the method comprising administering a compound describedherein.

In certain preferred aspects of the invention, any of the embodiments oraspects of the inventive compound of Formula I-VII that are describedherein can be used in the method of imaging. Representative examples ofpreferred compounds for use in the method are described in thespecification and the dependent claims of the instant application.

In certain preferred aspects, the compounds of the present invention areused as in vivo imaging agents of tissues and organs in variousbiomedical applications including, but not limited to, tomographicimaging of organs, monitoring of organ functions, coronary angiography,fluorescence endoscopy, imaging of tumors, laser guided surgery,photoacoustic and sonofluorescence methods, and the like. In one aspect,the compounds of the invention are useful for the detection of thepresence of tumors and other abnormalities by monitoring the bloodclearance profile of the dyes. In another aspect of the invention, thecompounds are useful for laser assisted guided surgery for the detectionof micro-metastases of tumors upon laparoscopy. In yet another aspect,the compounds are useful in the diagnosis of atherosclerotic plaques andblood clots.

In further aspects, the compounds of the present invention are used inthe imaging of: (1) ocular diseases in ophthalmology, for example, toenhance visualization of chorioretinal diseases, such as vasculardisorders, retinopathies, neovascularization, and tumors via directmicroscopic imaging; (2) skin diseases such as skin tumors via directmicroscopic imaging; (3) gastrointestinal, oral, bronchial, cervical,and urinary diseases and tumors via endoscopy; (4) atheroscleroticplaques and other vascular abnormalities via flexible endocsopiccatheters; (5) breast tumors via 2D- or 3D-image reconstruction; and (6)brain tumors, perfusion, and stroke via 2D- or 3D-image reconstruction.

In certain aspects, the compounds of the invention that arebioconjugates are particularly useful for imaging tumors, tissues, andorgans in a subject. For example, the existence of cancer cells orcancer tissues can be verified by labeling an anti-tumor antibody with acompound of Formula I-VII and then administering the bioconjugatedantibody to the subject for detection and imaging of the tumor.Conjugates between the dye compound and other antibodies, peptides,polypeptides, proteins, ligands for cell surface receptors, smallmolecules, and the like are also useful agents for the in vivo imagingof tumors, tissues, and organs in a subject.

In certain aspects, the compounds of the invention may be administeredeither systemically or locally to the organ or tissue to be imaged,prior to the imaging procedure. In one aspect, the compounds areadministered intravenously. In another aspect, the compounds areadministered parenterally. In yet another aspect, the compounds areadministered enterally. The compositions used for administration of thecompound typically contain an effective amount of the compound orconjugate along with conventional pharmaceutical carriers and excipientsappropriate for the type of administration contemplated. For example,parenteral formulations advantageously contain a sterile aqueoussolution or suspension of a compound of Formula I-VII or a bioconjugatethereof. Compositions for enteral administration typically contain aneffective amount of the compound or bioconjugate in aqueous solution orsuspension that may optionally include buffers, surfactants, thixotropicagents, flavoring agents, and the like.

In certain aspects, the compositions are administered in doses effectiveto achieve the desired optical image of a tumor, tissue, or organ. Suchdoses may vary widely, depending upon the particular compound orbioconjugate employed, the tumor, tissue, or organ subjected to theimaging procedure, the imaging equipment being used, and the like.

In an alternative aspect, the method of the present invention providesfor administering to the subject a therapeutically effective amount of acompound; a targeting agent, such as a bioconjugate; or mixturesthereof. In one aspect, the targeting agent selectively binds to thetarget tissue. Light at a wavelength or waveband corresponding to thatwhich is absorbed by the photosensitizing agent is then administered. Inanother aspect, the compounds of the present invention act agentscapable of binding to one or more types of target cells or tissues, whenexposed to light of an appropriate waveband, absorb the light, causingsubstances to be produced that illuminate, impair or destroy the targetcells or tissues. Preferably, the compound is nontoxic to the subject towhich it is administered or is capable of being formulated in a nontoxiccomposition that can be administered to the subject. In addition,following exposure to light, the compound in any resulting photodegradedform is also preferably nontoxic.

In yet another aspect, the compounds of the present invention areadministered by any means known in the art, including, but not limitedto, ingestion, injection, transcutaneous administration, transdermaladministration, intravenously, subcutaneously and the like. Preferably,the compounds are administered transcutaneously, intravenously,subcutaneously, or intramuscularly to a subject.

In certain aspects, during imaging, the light passes through unbrokentissue. Where the tissue layer is skin or dermis, such transcutaneousimaging includes transdermal imaging, and it will be understood that thelight source is external to the outer skin layer. In some aspects (i.e.,transillumination), the light passes through a tissue layer, such as theouter surface layer of an organ (e.g., the liver). In such cases, thelight source is preferably external to the organ, but internal orimplanted within the subject or patient.

In further aspects of the invention, the target tumor, tissue, or organfor treatment is selected from the group of vascular endothelial tissue,an abnormal vascular wall of a tumor, a solid tumor, a tumor of thehead, a tumor of the neck, a tumor of a the gastrointestinal tract, atumor of the liver, a tumor of the breast, a tumor of the prostate, atumor of the ovary, a tumor of the uterus, a tumor of the testicle, atumor of the lung, a nonsolid tumor, malignant cells of one of ahematopoietic tissue and a lymphoid tissue, lesions in the vascularsystem, a diseased bone marrow, neuronal tissue or diseased neuronaltissue, and diseased cells in which the disease is one of an autoimmuneand an inflammatory disease. In yet a further aspect, the target tissueis a lesion in the vascular system of a type selected from the group ofatherosclerotic lesions, arteriovenous malformations, aneurysms, andvenous lesions.

In certain embodiments, the compounds of Formula I-VII can be used inthe detection of reactive oxygen species. In certain instances, themethods herein can be used to diagnose a disease or disorder such ascarotid artery injuries, atherosclerosis, hypertension, cancers,diseases and disorders characterized by inflammation, radiation-inducedlate normal tissue damage; tissue damages due to chemotherapy,reperfusion after ischemia, or transplantation; diabetes, such as type 1diabetes (T1D), neurodegenerative diseases, such as Alzheimer's disease,Parkinson's disease, ALA, and Huntington's disease; cerebrovasculardisease, cystic fibrosis, chronic kidney disease, cardiovasculardisease, preeclampsia, diseases of the eye, and combinations thereof.

In one embodiment, the present invention provides a method for detectinga reactive oxygen species, the method comprising: contacting a cell withone or more compounds of Formula I-VII to form an oxidized form of thecompound; and exciting the oxidized form of the compound to emit light.

In still further aspects, the forms of energy include, but are notlimited to, light (i.e., radiation), thermal, sonic, ultrasonic,chemical, light, microwave, ionizing (such as x-ray and gamma ray),mechanical, and electrical. The term “radiation” as used herein includesall wavelengths and wavebands. Preferably, the radiation wavelength orwaveband is selected to correspond with or at least overlap thewavelengths or wavebands that excite the photosensitizing agent.Compounds of the instant invention typically have one or more absorptionwavebands that excite them to produce the substances which illuminate,damage or destroy target cells, tissues, organs, or tumors. Preferably,the radiation wavelength or waveband matches the excitation wavelengthor waveband of the photosensitizing agent and has low absorption by thenon-target cells and the rest of the subject, including blood proteins.More preferably, the radiation wavelength or waveband is within the NIRrange of about 600 nm to about 1000 nm or a related range thereof (e.g.,the ranges that are described in the instant claims).

In certain aspects, the compounds of the present invention are used todirectly stain or label a sample so that the sample can be identified orquantitated. For instance, such compounds can be added as part of anassay for a biological target analyte, as a detectable tracer element ina biological or non-biological fluid; or for such purposes asphotodynamic therapy of tumors, in which a dyed sample is irradiated toselectively destroy tumor cells and tissues; or to photoablate arterialplaque or cells, usually through the photosensitized production ofsinglet oxygen.

Typically, the sample is obtained directly from a liquid source or as awash from a solid material (organic or inorganic) or a growth medium inwhich cells have been introduced for culturing, or a buffer solution inwhich cells have been placed for evaluation. Where the sample comprisescells, the cells are optionally single cells, including microorganisms,or multiple cells associated with other cells in two or threedimensional layers, including multicellular organisms, embryos, tissues,biopsies, filaments, biofilms, and the like.

A detectable optical response as used herein includes a change in, oroccurrence of, an optical signal that is detectable either byobservation or instrumentally. Typically the detectable response is achange in fluorescence, such as a change in the intensity, excitation oremission wavelength distribution of fluorescence, fluorescence lifetime,fluorescence polarization, or a combination thereof. The degree and/orlocation of staining, compared with a standard or expected response,indicates whether and to what degree the sample possesses a givencharacteristic. Some compounds of the invention may exhibit littlefluorescence emission, but are still useful as quenchers or chromophoricdyes. Such chromophores are useful as energy acceptors in FRETapplications, or to simply impart the desired color to a sample orportion of a sample.

FRET is a process by which a donor molecule (e.g., a dye) absorbs light,entering an excited state. Rather than emitting light, the firstmolecule transfers its excited state to a acceptor molecule with otherproperties (e.g., a dye fluorescing at a different wavelength or aquencher), and the acceptor fluoresces or quenches the excitation.Because the efficiency of the transfer is dependant on the twomolecules' proximity, it can indicate information about molecularcomplex formation or biomolecular structure. It can also indicate wherea particular complex is located within a cell or organism (e.g., FREToptical microscopy). For ways to use similar dyes as acceptors(quenchers) in FRET processes, see X. Peng, H. Chen, D. R. Draney, W.Volcheck, A. Schultz-Geschwender, and D. M. Olive, “A nonfluorescent,broad-range quencher dye for Förster resonance energy transfer assays,”Anal. Biochem 2009, 388(2): 220-228.

In certain aspects, for biological applications, the compounds of theinvention are typically used in an aqueous, mostly aqueous, oraqueous-miscible solution prepared according to methods generally knownin the art. The exact concentration of compound is dependent upon theexperimental conditions and the desired results, but ranges of 0.00001mM up to 0.1 mM, such as about 0.001 mM to about 0.01 mM, are possible.The optimal concentration is determined by systematic variation untilsatisfactory results with minimal background fluorescence isaccomplished.

In certain aspects, the method may involve treatment of an animal orsample with a dose comprising a compound of Formula I-VII, or abioconjugate thereof, or any of the aspects or embodiments thereof. Theexact concentration of compound is dependent upon the subject and thedesired results. In certain embodiments, a dose of at least about 0.001,0.005, 0.01, 0.025, 0.05, or 0.075 mg/kg is used. Alternatively, a doseof at most about 0.001, 0.005, 0.01, 0.025, 0.05, or 0.075 mg/kg isused. In certain other embodiments, a dose of at least about 0.1, 0.25,0.5, or 0.75 mg/kg is used. Alternatively, a dose of at most about 0.1,0.25, 0.5, or 0.75 mg/kg is used. In still other embodiments, a dose ofat least about 0.1, 0.25, 0.5, or 0.75 mg/kg is used. Alternatively, adose of at most about 0.1, 0.25, 0.5, or 0.75 mg/kg is used. In yetstill other embodiments, a dose of at least about 1, 2.5, 5, or 7.5mg/kg is used. Alternatively, a dose of at most about 1, 2.5, 5, or 7.5mg/kg is used. In additional other embodiments, a dose of at least about10, 25, 50, or 75 mg/kg is used. Alternatively, a dose of at most about10, 25, 50, or 75 mg/kg is used. In additional still other embodiments,a dose of at least about 100, 250, 500, or 750 mg/kg is used.Alternatively, a dose of at most about 100, 250, 500, or 750 mg/kg isused. Other amounts for administration of an effective dose may bereadily determined by one of skill in the art.

In certain aspects, in vitro, the compounds are advantageously used tostain samples with biological components. The sample can compriseheterogeneous mixtures of components (e.g., mixtures including intactcells, fixed cells, cell extracts, bacteria, viruses, organelles, andcombinations thereof), or a single component or homogeneous group ofcomponents (e.g. natural or synthetic amino acid, nucleic acid orcarbohydrate polymers, or lipid membrane complexes). Within theconcentrations of use, these compounds are generally non-toxic to livingcells and other biological components.

The compound is combined with the sample in any way that facilitatescontact between the compound and the sample components of interest.Typically, the compound or a solution containing the compound is simplyadded to the sample. Certain compounds of the invention, particularlythose that are substituted by one or more sulfonic acid moieties, tendto be impermeant to membranes of biological cells, and once insideviable cells, they are typically well-retained. Treatments thatpermeabilize the plasma membrane, such as electroporation, shocktreatments or high extracellular ATP, can be used to introduce selectedcompounds into cells. Alternatively, selected dye compounds can bephysically inserted into cells, e.g., by pressure microinjection, scrapeloading, patch clamp methods, or phagocytosis.

Alternatively, dye compounds can be conjugated to a biomolecule thatincreases their uptake into cells (e.g., cell-penetrating peptides suchas Tat, penetratin, transportin, derivatives thereof (e.g., Tatderivatives incorporating β- and γ-amino acids), and the like). Thisgeneral approach is usable in vitro or in vivo.

In certain aspects, at any time after or during staining, the sample isilluminated with a wavelength of light selected to give a detectableoptical response, and observed with a means for detecting the opticalresponse. Equipment that is useful for illuminating the compounds of theinvention includes, but is not limited to, hand-held ultraviolet lamps,mercury arc lamps, xenon lamps, lasers and laser diodes. Theseillumination sources are optionally integrated into laser scanners,fluorescence microplate readers, standard or minifluorometers, orchromatographic detectors. Preferred aspects of the invention arecompounds that are excitable at or near the wavelengths 633-636 nm, 647nm, 649 nm, 651 nm, 647-651 nm, 660 nm, 674 nm, 675 nm, 678 nm, 680 nm,674-680 nm, 685 nm, 674-685 nm, 680-685 nm, 685-690 nm, 690-695 nm,690-700 nm, and beyond 700 nm, such as 780 nm, 810 nm and 850 nm, asthese regions closely match the output of exemplary compounds or ofrelatively inexpensive excitation sources.

The optical response is optionally detected by visual inspection, or byuse of any of the following devices: CCD cameras, video cameras,photographic film, laser-scanning devices, fluorometers, photodiodes,quantum counters, epifluorescence microscopes, scanning microscopes,flow cytometers, fluorescence microplate readers, or by means foramplifying the signal such as photomultiplier tubes. Where the sample isexamined by means of a flow cytometer, examination of the sampleoptionally includes sorting portions of the sample according to theirfluorescence response.

VII. Immunoassay Methods

In certain embodiments, the present invention concerns immunodetectionmethods for binding, purifying, removing, quantifying and/or otherwisegenerally detecting biological antigens. Commonly employedimmunodetection methods include enzyme linked immunosorbent assay(ELISA), Western blotting, radioimmunoassay (RIA), immunoradiometricassay, fluoroimmunoassay, chemiluminescent assay, and bioluminescentassay. The steps of various useful immunodetection methods have beendescribed in the scientific literature, such as, e.g., Doolittle M H andBen-Zeev O, 1999; Gulbis B and Galand P, 1993; De Jager R et al., 1993;and Nakamura et al., 1987, each incorporated herein by reference.

Chemiluminescence based detection has been the method of choice for theimmunodetection methods such as Western blotting and ELISA, but thesensitivity of the analysis is compromised as the accumulation of signalintensity is not possible in chemiluminescence. The present inventionprovides novel near infrared (near-IR) chemifluorescent substrates thatgenerate fluorescence signals upon activation by enzyme-antibodyconjugates. The signal accumulates with each turnover by the enzyme andleads to advantageously high assay sensitivity.

Hydro/deuterocyanines are hydrophobic molecules and will stick to ablotting membrane (e.g., a nitrocellulose membrane), but they arenon-fluorescent and will not emit light. Secondary antibody-HRPconjugates bound to protein bands on the membrane oxidize thehydrocyanine or deuterocyanines to their parent fluorescent cyanine dyestructure, however, and consequently the bands will emit fluorescentsignals. See FIG. 14. Because of the transient nature of the hydroxylradical formed by the reaction of hydrogen peroxide and the antibody HRPconjugates, the radicals oxidize only the hydro/deuterocyanines presentin the close proximity to the protein bands on the membrane and,therefore, the fluorescence signals are compact. Furthermore, theoxidized fluorescent molecules accumulate with each turn over by the HRPenzyme. The oxidized molecule is also hydrophobic and therefore, sticksto the hydrophobic membrane and hence, the sensitivity is better thanchemiluminescence or secondary antibody detection methods.

The group of antigens which can be used for carrying out immunologicalassays is extensive and includes human biopsy material, mammalian tissueor cells, bodily fluids, mycoplasma, metazoan parasites, fungi,bacterial, protozoa, viruses, or preparations derived from any of these.Apart from the antigens described in the Examples, the following arealso suitable: viruses (or antigens prepared from viruses) such asinfluenza strains, including A, A₁, A₂, B, C, parainfluenza strains,including 1, 2 or 3, lymphocytic choriomeningitis virus, mumps, Q feverrickettsia, rabies, respiratory syncytial virus, Rotavirus, Rubella,Adenovirus, Epstein-Barr virus, Brucella, Hepatitis B, Cocksackie B1-B6,A9, Polio 1, 2 or 3, Reo, Echo 1-33; fungal antigens, such asHistoplasmosa capsulatum, Coccidioides immitis, Blastomycesdermatitidis, Aspergillus fumigatus, Aspergillus flavus and Aspergilluscarneus; parasitic antigens, such as Entemeba histolytica, Trypanosomacruzi, Echinococcus granulosis, Schistosoma mansoni; bacterial antigens,such as Spirochete reiter, Treponema pallidum, Escherichia coli,Leptospira, Listeria, Salmonella, Shigella, Staphylococci, Streptococci,and Legionella pneumophila; auto-antigens, such as nuclearribonucleicprotein, complement fractions, human serum proteins,rheumatoid factor, insulin, insulin receptor, thyroid stimulatinghormone receptor, acetylcholine receptor and other hormones, receptorsor allergens.

The present invention can also be used in the detection and monitoringof antigens of other kinds, such as drugs and hormones. Such tests applyspecific antibodies to a support, and detect and quantitate specificantigens by the inverse of the immunoassay procedures described above.The property of complement proteins to bind specifically toantigen-antibody complexes may then be used directly or indirectly tovisualize and quantitate the specific antigens, such as drugs or otherpharmacological reagents, or hormones, or any desired combination ofsuch antigens.

Immunoassay formats useful in the present invention include Westernblots, enzyme-linked immunosorbent assays (ELISAs), and dot-blots. Ingeneral, the methods involve binding of an antigen of interest directlyor indirectly to a solid support. The solid support may be any materialwith sufficient surface porosity to allow access by detection antibodiesand a suitable surface affinity to bid antigens. Microporous structuresare generally preferred, but materials with gel structure in thehydrated state may be used as well. Useful solid supports include:natural polymeric carbohydrates and their synthetically modified,cross-linked or substituted derivatives, such as agar, agarose,cross-linked alginic acid, substituted and cross-linked guar gums,cellulose esters, especially with nitric acid and carboxylic acids,mixed cellulose esters, and cellulose ethers; natural polymerscontaining nitrogen, such as proteins and derivatives, includingcross-linked or modified gelatin; natural hydrocarbon polymers, such aslatex and rubber; synthetic polymers which may be prepared with suitablyporous structures, such as vinyl polymers, including polyethylene,polypropylene, polystyrene, polyvinylchloride, polyvinylacetate and itspartially hydrolyzed derivatives, polyacrylates, polyacrylamides,polymethacrylates, copolymers and terpolymers of the abovepolycondensates, such as polyesters, polyamides, and other polymers,such as polyurethanes or polyepoxides; porous inorganic materials suchas sulfates or carbonates of alkaline earth metals and magnesium,including barium sulfate, calcium sulfate, calcium carbonate, magnesiumcarbonate, silicates of alkali and alkaline earth metals, aluminum andmagnesium; and aluminum or silicon oxides or hydrates, such as clays,alumina, talc, kaolin, zeolite, silica gel, or glass (These materialsmay be used as fillers with the above polymeric materials); and mixturesor copolymers of the above classes, such as graft copolymers obtained byinitiating polymerization of synthetic polymers on a pre-existingnatural polymer.

These materials can be used in suitable shapes, such as films, sheets,plates, and wellplates, or they may be coated onto or bonded orlaminated to appropriate inert carriers, such as paper, glass, plasticfilms, or fabrics. The porous structure of nitrocellulose, inparticular, has excellent absorption and adsorption qualities for a widevariety of reagents which may be used in the methods of the invention.Nylon also possess similar characteristics and is a suitable supportmaterial.

Once the selected antigens have been bound onto the solid support, thesupport can be processed to block excess binding sites of the porousmaterial before proceeding. This can be done by incubation of thesupport containing the antigens with non-specific proteins or with amixture of such proteins, or with total serum, or any combination ofthese ingredients alone or together. Proteins or other agents used forblocking should not interfere or cross-react with any of the antibodiesor antigens in the immunoassays, and they should be different from thosemounted on the support.

A. Western Blotting

Western blotting is an accurate method of assaying for the presence of aparticular protein antigen within a biological sample. The generalmethodology of the Western blot includes applying the sample to apolyacrylamide gel and separating the proteins through the technique ofgel electrophoresis. The proteins, having been separated into discretebands, are subsequently transferred to a sheet (e.g., nitrocellulose)using an electrophoretic blotting chamber. Once the protein bands havebeen transferred, the blot is treated with a primary antibody specificto the particular antigen of interest; if the antigen is present, theprimary antibody will bind to the antigen. The primary antibody can bean enzyme-antibody conjugate, wherein the enzyme is capable of oxidizingthe hydro/deuterocyanine probes of the present invention. Free antibodyis washed away, and the enzyme linked to the antibody can then in turnreact with the hydro/deuterocyanine probe applied to the blot which thengenerates a fluorescent signal. Alternatively, the primary antibody canbe bound by secondary antibody-enzyme conjugate. The blot is rinsedagain to remove excess secondary antibody-enzyme conjugate, and theenzyme linked to the secondary antibody may then in turn react with thehydro/deuterocyanine probe applied to the blot. The presence of verysmall quantities of antigen may thus be detected due to the highlysensitive nature of the Western blotting technique.

Alternatively, in another embodiment, the present invention provides amultiplex detection immunoassay utilizing, for example, H-IR780F2 todetect the presence of HRP, and an alkaline phosphatase at differentwavelengths by utilizing on the one hand HRP labeled proteins and on theother hand alkaline phosphatase labeled proteins. In yet anotherembodiment, a fluorescently labeled protein and an HRP labeled proteincould be simultaneously detected at different wavelengths.

A Western blot membrane is prepared by denaturing and solubilizing asample in a sample buffer containing sodium dodecyl sulfate, Tris bufferand other components, and electrophoresed in a polyacrylamide gelfollowing established procedures (e.g., Laemmli gel procedure). Theresolved proteins are electrophoretically transferred from the gel to anitrocellulose membrane by established procedures (Towbin, H. et al.,PNAS (USA) 76: 4350-4354 (1979)) and the membrane is saturated withnon-specific protein (e.g., solubilized nonfat milk powder). Themembrane can then be cut into individual strips for incubation withserum samples, or incubated without cutting. Upon following the typicalWestern blot processing as described above, bands appear on membraneswhich have been exposed to serum containing antibodies to the antigen ofinterest. Reactive non-specific bands without diagnostic significancemay also be observed in sera from normal, healthy individuals in certaininstances; known bands correlating with seropositivity for the antigenof interest can be determined by other assays so as to properlydistinguish them from the non-specific bands if necessary.

A dot-blot procedure can also be used for the immunoassays of thepresent invention. The dot-blot procedure generally includes applyingantibody, which is specific to the antigen of interest, directly to amembrane. The membrane is then washed to remove unbound antibody. Thesample containing the antigen of interest is then applied to themembrane, and the antigen subsequently binds to the antibody attached tothe membrane. The membrane is again washed to remove unbound molecules,treated with a second antibody specific to a different site on theantigen of interest, and washed to remove unbound enzyme conjugate. Thisantibody is linked to an enzyme which reacts with a hydro/deuterocyaninesubstrate to generate a fluorescent signal. The signals appear as dots,rather than bands as in the Western blot, since antigen is applied tothe support in a single drop rather than as electrophoretically resolvedbands of protein.

The membrane is processed with a serum sample in the same manner as aconventional Western blot membrane as known to those skilled in the art.In a preferred embodiment, the following steps are performed: 1)incubation of the membrane with diluted serum; 2) buffer wash to removeunbound antibody; 3) incubation with enzyme-conjugatedanti-immunoglobulin; 4) buffer wash to remove unbound enzyme conjugate;and 5) incubation with enzyme substrate.

B. Enzyme-Linked Immunosorbent Assay

Enzyme-linked immunosorbent assays (ELISAs), can be performed by fixinga reference antigen to a solid phase support. A biological samplesuspected of containing the antigen (and primary antibodies to theantigen), can be mixed with a labeled reagent (such as secondaryantibody-enzyme conjugate that bind the primary antibodies), andincubated with the fixed antigen. Alternatively, the binding of theprimary antibodies to the fixed antigen to form a fixed-antigen/primaryantibody duplex can be conducted in a first step. Binding of the duplexby the secondary antibody-enzyme conjugate can then be conductedseparately in a second step. In either case, the biological samples andsolid support undergo a series of dilution, incubation, and washingsteps in order to separate bound and free antibodies. The process isgenerally concluded with a detection step to indirectly measure theamount of antibody (or antigen) in the test sera. Determining thepresence of an antigen in a biological sample by detecting antibodies tothe antigen has been characterized as an “indirect” ELISA. In the caseof ELISAs conducted with a secondary antibody-peroxidase conjugate, forexample, the detection step can include reaction of a bound conjugatewith a hydro/deuterocyanine substrate and hydrogen peroxide to produce adetectable fluorescent signal.

The ELISA assay can also be a “sandwich” ELISA. In this assay, anantibody specific to an antigen of interest is fixed to a solid phase orsupport, and the fixed antibody is then contacted with a sample beingtested for the antigen. If the antigen is present in the sample, atleast a portion of the antigen will be extracted from the sample viabinding by the fixed antibody to form a fixed-antibody/antigen duplex.After a suitable incubation period, the solid support can be washed toremove the residue of the fluid sample and contacted with a solutioncontaining a known quantity of a primary antibody that binds to thefixed-antibody/antigen duplex. The primary antibody can be anantibody-peroxidase conjugate, and detection sing a hydro/deuterocyaninesubstrate can be detected as described above.

Alternatively, detection of fixed-antibody/antigen complexes can beconducted using a multi-step approach. A fixed-antibody/antigen/primaryantibody complex can be detected, for example, using a secondaryantibody-enzyme conjugate that has binding affinity for the primaryantibody. After processing as described above, detection of thesecondary antibody can be conducted using a hydro/deuterocyaninesubstrate. Alternatively, an unlabeled secondary antibody can be usedand detected using a third binding ligand or antibody that is linked toa detectable enzyme. Multi-step procedure can provide high selectivityand low background for sensitive applications. Still other reagentscapable of selectively binding or detecting antibody/antigen complexescan also be used in the ELISA assays. Such reagents include, but are notlimited to, antibodies or other ligands that can be labeled using avariety of markers, e.g., a biotin/avidin binding pair, as is known inthe art. Suitably labeled second and third antibodies can also be used.

The ELISA can also be a “competitive” ELISA. In this assay, a knownquantity of a primary antibody to a particular antigen is added to abiological sample suspected of containing the antigen. The biologicalmixture is incubated under conditions sufficient to form primaryantibody/antigen complexes; the biological mixture will generallycontain a certain amount of free primary antibody. Meanwhile, a knownquantity of the antigen is fixed to a solid support. The support withthe fixed-antigen is contacted with the biological mixture containingthe primary antibody/antigen complexes and the free primary antibody.Different levels of free primary antibodies will be available forbinding to the fixed-antigen on the solid support, depending on thequantity of the antigen in the original biological sample. Detection offixed-antigen/primary antibody complexes can be conducted with secondand third antibodies as described above. The quantity of the antigen inthe original biological sample can be determined based on the amount ofthe primary antibodies detected using the competitive ELISA.

In terms of antigen, antibody or antibody/antigen complex detection, thebiological sample analyzed may be any sample that is suspected ofcontaining an antigen or antigen/antibody complex, such as, for example,a tissue section or specimen, a homogenized tissue extract, a cell, anorganelle, separated and/or purified forms of any of the aboveantigen-containing compositions, or any biological fluid that comes intocontact with the cell or tissue, including blood and/or serum.

Irrespective of the format employed, ELISAs have certain features incommon, such as coating, incubating and binding, washing to removenon-specifically bound species, and detecting the bound immunecomplexes. A fixed antigen or antibody is generally contacted with achosen biological sample under effective conditions and for a period oftime sufficient to allow the formation of immune complexes. After thistime, the ELISA plate can be washed to remove any non-specifically boundspecies, allowing only specifically-bound immune complexes to bedetected. One of skill in the art will recognize that such techniquescan also be applied to tissue sections, dot blots, or Western blots asthey are to ELISA plates.

In coating a plate with either antigen or antibody, wells of the platecan be incubated with a solution of the antigen or antibody, eitherovernight or for a specified period of hours. The wells of the plate canthen be washed to remove incompletely adsorbed material. Any remainingavailable surfaces of the wells can then be “blocked” with a nonspecificprotein that is antigenically neutral with regard to the test antisera.Blocking agents include, but are not limited to, bovine serum albumin(BSA), casein, or solutions of milk powder. Blocking can preventnonspecific adsorption sites on the immobilizing surface and reduce thebackground caused by nonspecific binding of antisera onto the surface.

After binding of a protein or antibody to the well, blocking, andwashing to remove unbound material, the immobilizing surface isgenerally contacted with the biological sample to be tested underconditions effective to allow immune complex (antigen/antibody)formation. Detection of the immune complex then requires a labeledsecondary binding ligand or antibody, and a secondary binding ligand orantibody in conjunction with a labeled tertiary antibody or a thirdbinding ligand.

Biological samples and antibody/antigen compositions can be diluted withsolutions such as BSA, bovine gamma globulin (BGG), or phosphatebuffered saline (PBS)/Tween. These added agents can assist in thereduction of nonspecific background. Incubation is generally conductedat a temperature or for a period of time sufficient to allow effectivebinding. For example, incubation can be conducted for about 1 to 4 hoursat temperatures around 25° C., or for overnight at around 4° C.

Following all incubation steps in an ELISA, the contacted surface iswashed so as to remove non-complexed material. Such procedures caninclude washing with a solution such as PBS/Tween or borate buffer.Following the formation of fixed-antibody/antigen complexes andsubsequent washing, the occurrence of even minute amounts of immunecomplexes may be determined. To provide a detecting means, a second orthird antibody can be conjugated to an enzymatic label to allow fordetection using hydro/deuterocyanine substrates as described above.Conditions that favor the development of further immune complexformation are generally used for binding of the fixed-antibody/antigencomplex by additional antibodies (e.g., incubation for 2 hours at roomtemperature in a PBS-containing solution such as PBS-Tween).

In certain instances, the hydrocyanines are useful in imaging ROS indiverse biological experiments. Certain of the reduced dyes disclosedherein (e.g., compounds 1 and 2 of Table 1) are cell permeable withimproved water solubility. In addition, the use of the Schlenk techniquegenerates longer storage life. In certain instances, the use of DMSOincreases the shelf life of the inventive compounds.

It also is contemplated that reagents may be packaged in a kit that maybe produced commercially to measure the soluble antigens, antibodies orantibody/antigen complexes described herein.

The compounds described herein are suitable for use in enzymehistochemistry, immunohistology, immunocytochemistry, immunoassays,immunofluorescent assays, immunoprecipitation assays, ELISA, flowcytometry, fluorescent activated cell sorting, radioimmunochemistry,electrophoresis, two-dimensional gel electrophoresis, Western blotting,protein sequencing, mass spectrometry, proteomic analysis, and proteinmicroarray analysis. With regard to protein microarray analysis, aproduct from R&D Systems known as the Proteome Profiler™ 96 Phospho-RTKArray 1 is suitable for use. The Proteome Profiler 96 Human Phospho-RTKArray 1 (Catalog # ARZ001) employs a two-site sandwich immunoassaytechnique to simultaneously detect multiple analytes (e.g., 16phosphorylated receptor tyrosine kinases) in a single sample of celllysate. Multiple capture antibodies that specifically recognize thetarget detected by the assay are spotted into each well of a 96-wellmicroplate.

VIII. Examples

The following examples are offered to illustrate, but not to limit theclaimed invention.

Example 1

IR780, IRDye® 800CW, or IRDye® 680RD (0.2 mmol) (each commerciallyavailable) is dissolved in 5 ml of methanol. The mixture is placed in a25-ml flask covered with aluminum foil. Sodium borohydride (3 mg, 0.08mmol in 0.5 ml methanol) is slowly added dropwise to the cyanine dyesolution for reduction. After the addition is complete, the mixture isstirred for 10 minutes or until monitoring revealed that the reaction iscomplete. The reaction mixture is stirred an additional 10 minutesbefore removing the solvent under reduced pressure. The crude product isthen purified by silica gel chromatography using hexanes/ethyl acetateas the eluent.

Deuterocyanines are prepared using the procedure above except sodiumborohydride is replaced with sodium borodeuteride (i.e., NaBD₄).

Example 2 Preparation of Sodium2-((1E,3Z,5E)-3-Bromo-5-(1,1-dimethyl-6,8-disulfonato-3-(3-sulfonatopropyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate

Sodium2-((1E,3Z,5E)-3-Bromo-5-(1,1-dimethyl-6,8-disulfonato-3-(3-sulfonatopropyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate(1)

A 100 ml round bottom flask fitted with a reflux condenser was chargedwith sodium1,1,2-trimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate(565 mg, 1 mmol),(E)-N—((Z)-2-bromo-3-(phenylamino)allylidene)benzenaminium bromide (150mg, 0.5 mmol), and pyridine (1 ml). Acetic anhydride (10 ml) was addedto the flask, and the mixture was heated at 115° C. for 2 h, cooled toroom temperature, and diluted with 25 ml of ethyl ether. The resultingdark blue dye precipitate was collected by filtration, then dissolved in20 ml of water and purified by preparative reverse-phase HPLC to affordthe compound 1 as a blue powder (285 mg, 50%; UV/vis absorption max 674nm).

Example 3 Preparation of Sodium2-((1E,3Z,5E)-3-Bromo-5-(1,1-dimethyl-6,8-disulfonato-3-(3-sulfonatobutyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatobutyl)-1H-benzo[e]indolium-6,8-disulfonate

Sodium2-((1E,3Z,5E)-3-Bromo-5-(1,1-dimethyl-6,8-disulfonato-3-(3-sulfonatobutyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatobutyl)-1H-benzo[e]indolium-6,8-disulfonate(2)

Compound 2 was prepared analogously to compound 1 (Example 2).

Example 4 Preparation of Sodium2-((1E,3Z,5E)-3-(3-(4-Carboxybutyl)phenyl)-5-(1,1-dimethyl-6,8-disulfonato-3-(3-sulfonatopropyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate

Sodium2-((1E,3Z,5E)-3-(3-(4-Carboxybutyl)phenyl)-5-(1,1-dimethyl-6,8-disulfonato-3-(3-sulfonatopropyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate(3)

Compound 1 (80 mg), 3-(4-carboxybutyl)phenylboronic acid (40 mg), andcesium carbonate (20 mg) are stirred into 1:1 water:ethanol (10 ml)under nitrogen at room temperature.Tetrakis(triphenylphosphine)palladium(0) (10 mg) is added to thereaction mixture. The mixture was refluxed for 4 hours, and the solventand volatile compounds are evaporated under vacuum. The crude product ispurified by flash chromatography on reverse-phase C18-functionalizedsilica by eluting with a 1:4 acetonitrile:water mixture. The purifiedproduct 3 has UV/vis absorption max of λ_(MeOH)=680 nm, ε=229,000;λ_(PBS)=676 nm, ε=239,000.

Example 5 Preparation of Sodium2-((1E,3Z,5E)-5-(1,1-Dimethyl-6,8-disulfonato-3-(3-sulfonatopropyl)-1H-benzo[e]indol-2(3H)-ylidene)-3-(3-(5-(2,5-dioxopyrrolidin-1-yloxy)-5-oxopentyl)phenyl)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate

Sodium2-((1E,3Z,5E)-5-(1,1-Dimethyl-6,8-disulfonato-3-(3-sulfonatopropyl)-1H-benzo[e]indol-2(3H)-ylidene)-3-(3-(5-(2,5-dioxopyrrolidin-1-yloxy)-5-oxopentyl)phenyl)penta-1,3-dienyl)-1,1-dimethyl-3-(3-sulfonatopropyl)-1H-benzo[e]indolium-6,8-disulfonate(4)

To a solution of compound 3 (200 mg) in dry DMSO (15 ml) was addeddiisopropylethylamine (150 μL) and N,N′-disuccinimidyl carbonate (82mg). The mixture was stirred at room temperature for 2 hours and thenprecipitated into diethyl ether (200 mL). The crude reaction mixture waspurified on reverse-phase silica gel using acetonitrile/water eluent toyield the succinimidyl ester (120 mg, 60%).

Example 6 Preparation of Sodium2-((1E,3Z,5E)-3-(3-(2-Carboxyethyl)phenyl)-5-(1,1-dimethyl-6,8-disulfonato-3-(4-sulfonatobutyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(4-sulfonatobutyl)-1H-benzo[e]indolium-6,8-disulfonate

Sodium2-((1E,3Z,5E)-3-(3-(2-Carboxyethyl)phenyl)-5-(1,1-dimethyl-6,8-disulfonato-3-(4-sulfonatobutyl)-1H-benzo[e]indol-2(3H)-ylidene)penta-1,3-dienyl)-1,1-dimethyl-3-(4-sulfonatobutyl)-1H-benzo[e]indolium-6,8-disulfonate(5)

Compound 5 was prepared analogously to compound 3, except that3-(3-boronophenyl)propionic acid is used as a starting material.

Example 7 Preparation of Sodium2-((1E,3Z,5E)-5-(1,1-Dimethyl-6,8-disulfonato-3-(4-sulfonatobutyl)-1H-benzo[e]indol-2(3H)-ylidene)-3-(3-(3-(2,5-dioxopyrrolidin-1-yloxy)-3-oxopropyl)phenyl)penta-1,3-dienyl)-1,1-dimethyl-3-(4-sulfonatobutyl)-1H-benzo[e]indolium-6,8-disulfonate

Sodium2-((1E,3Z,5E)-5-(1,1-Dimethyl-6,8-disulfonato-3-(4-sulfonatobutyl)-1H-benzo[e]indol-2(3H)-ylidene)-3-(3-(3-(2,5-dioxopyrrolidin-1-yloxy)-3-oxopropyl)phenyl)penta-1,3-dienyl)-1,1-dimethyl-3-(4-sulfonatobutyl)-1H-benzo[e]indolium-6,8-disulfonate(6)

Compound 6 was prepared using methods of the present invention usingcompound 5 as starting material.

Example 8 Preparation of Sodium(E)-2-((2Z,4E)-3-Bromo-5-(5-chloro-3,3-dimethyl-7-(3-sulfonatopropyl)-3H-pyrrolo[2,3-b]pyridin-7-ium-2-yl)penta-2,4-dienylidene)-3,3-dimethyl-1-(3-sulfonatopropyl)indoline-5-sulfonate(7)

Sodium(E)-2-((2Z,4E)-3-Bromo-5-(5-chloro-3,3-dimethyl-7-(3-sulfonatopropyl)-3H-pyrrolo[2,3-b]pyridin-7-ium-2-yl)penta-2,4-dienylidene)-3,3-dimethyl-1-(3-sulfonatopropyl)indoline-5-sulfonate(7)

A 100-mL round-bottom flask fitted with a reflux condenser was chargedwith3-(5-chloro-2,3,3-trimethyl-3H-pyrrolo[2,3-b]pyridin-7-ium-7-yl)propane-1-sulfonate(500 mg), sodium2,3,3-trimethyl-1-(3-sulfonatopropyl)-3H-indolium-5-sulfonate (500 mg),(E)-N—((Z)-2-bromo-3-(phenylamino)allylidene)benzenaminium bromide (100mg), sodium acetate (650 mg), and methanol (40 mL) were added to theflask. The mixture was heated at 50° C. for 5 h, allowed to cool to roomtemperature, and diluted with ethyl ether (25 mL). The resulting darkblue dye precipitate was collected by filtration, dissolved in water (20mL), and purified by preparative reverse-phase HPLC to afford the 7 as ablue powder (285 mg, 50%, UV 668 nm).

Example 9 Preparation of Sodium(E)-2-((2Z,4E)-3-(3-(2-Carboxyethyl)phenyl)-5-(5-chloro-3,3-dimethyl-7-(3-sulfonatopropyl)-3H-pyrrolo[2,3-b]pyridin-7-ium-2-yl)penta-2,4-dienylidene)-3,3-dimethyl-1-(3-sulfonatopropyl)indoline-5-sulfonate(8)

Sodium(E)-2-((2Z,4E)-3-(3-(2-Carboxyethyl)phenyl)-5-(5-chloro-3,3-dimethyl-7-(3-sulfonatopropyl)-3H-pyrrolo[2,3-b]pyridin-7-ium-2-yl)penta-2,4-dienylidene)-3,3-dimethyl-1-(3-sulfonatopropyl)indoline-5-sulfonate(8)

Compound 7 (80 mg), 3-(2-carboxyethyl)phenylboronic acid (40 mg), andcesium carbonate (20 mg) were stirred into water (20 mL) under nitrogenat room temperature. Tetrakis(triphenylphosphine)palladium (0) (10 mg)were added to the reaction mixture. The mixture was refluxed for 4 h,and the solvent and volatile compounds then were evaporated undervacuum. The crude product was purified by flash chromatography onreverse-phase silica with an acetonitrile/water mixture as the eluent.The purified compound had λ_(MeOH)=680 nm, λ_(PBS)=672 nm, ε=160,000.

TABLE 2 Absorption and Emission of Compound 8 Extinction Max. Abs. Max.Emis. Coefficient (nm) (nm) PBS 160,000 672 694 MeOH 170,000 680 694

Example 10

Reduced hydrocyanine dyes (H- or D-versions) are nonfluorescent, butturn fluorescent upon oxidation. This activation property was exploitedto utilize the reduced hydrocyanine dyes as horseradish peroxidase (HRP)substrates. In certain embodiments of an enzymatic assay, thehydrocyanines can be oxidized by HRP using hydrogen peroxide as theoxidizing agent, yielding a fluorescent signal. In some preferredembodiments, this fluorescent signal's wavelength can range from 530-900nm depending on the structure of the dye.

The following two dyes were synthesized and then tested in an enzymaticassay:

Synthesis of H-IR 780: To an oven-dried 250-mL round-bottomed flask witha stir-bar and septum under N₂ were added IR-780 (100 mg, 0.125 mmol),followed by methanol (100 mL). To the resulting green solution, sodiumborohydride (19.0 mg, 5.0 mmol) was slowly added over 5 min. Thesolution turned light yellow, and the mixture was stirred @ ambienttemperature for an additional 15 min. The solvent was removed underreduced pressure, and the product was purified by CombiFlash system(i.e., automated flash chromatography) using hexane/ethyl acetate aseluent.

Synthesis of D-IR 780: To an oven-dried 250-mL round-bottomed flask witha stir-bar and septum under N₂ were added IR-780 (100 mg, 0.125 mmol),followed by methanol (100 mL). To the resulting green solution, sodiumborodeuteride (21.0 mg, 5.0 mmol) was slowly added over 5 min. Thesolution turned light yellow, and the mixture was stirred @ ambienttemperature for an additional 15 min. The solvent was removed underreduced pressure, and the product was purified by CombiFlash systemusing hexane/ethyl acetate as eluent.

HRP 800 Assay Buffer: The HRP 800 Assay Buffer contains 60 μM HydrogenPeroxide, 0.2 μg/mL Acetanilide, 0.02% Triton X−100, in 100 mM CitrateBuffer, pH 3.0.

H-IR 780 Substrate solution: 10 μM H-IR 780 in the HRP 800 Assay Buffer.

D-IR 780 Substrate solution: 10 μM D-IR 780 in the HRP 800 Assay Buffer.

The utility of the H-IR 780 and D-IR 780 as a HRP substrate was testedby reaction of the dye with an enzyme-labeled antibody. The substrate,when oxidized by HRP and hydrogen peroxide, yields a fluorescent signalat approximately 800 nm in the NIR. Briefly, 100 μl of either H-IR 780substrate solution (B01-B12) or D-IR 780 substrate solution (C01-C12 andD01-D12) in the HRP assay buffer was added to the wells of 96-well platefollowed by the addition of 10 μl of goat anti-mouse HRP-labeledantibody (GAM-HRP) at a concentration of 0.8 μg/ml to 0.8 pg/ml. WellsB12, C12 and D12 received 10 μL of PBS buffer (pH 7.2) and were used asa control to measure the background fluorescence. The plate wasincubated at ambient temperature for 10 minutes and scanned using aLI-COR® Odyssey® imager (Channel: 800 nm, Sensitivity: 5, Focus Offset:3.5).

The results (FIG. 1) showed that the intensity of the fluorescencesignal increased with increasing concentration of GAM-HRP. Since thefluorescence response was dependent on the concentration of the GAM-HRP,proof of concept for use of hydrocyanine dyes as HRP substrates wasdemonstrated. This demonstrates the utility of H-IR-780 as a HRPsubstrate for an in-cell Western blot. FIG. 1 shows the usefulness ofH-IR-780 as an HRP substrate.

Example 11

Near-infrared (NIR) HRP substrates using hydrocyanine dyes have beentested and qualified using direct ELISA assays. The substrate, whenoxidized by HRP using hydrogen peroxide as the oxidizing agent, yields afluorescent signal at approximately 800 nm in the NIR.

Initial feasibility testing focused on optimizing individual assaybuffer components including pH and hydrogen peroxide concentration.Further testing considered the effects of substrate concentration, HRPenzyme concentration, surfactant selection and surfactant concentration(above and below the Critical Micelle Concentration). Once theseparameters were optimized, a direct ELISA assay was performed.

Briefly, serially diluted Rabbit IgG was immobilized (via adsorption tothe surface) on a high binding 96-well plate. Unbound IgG was removedand any remaining binding sites on the plate surface were blocking usingSuperblock (ThermoFisher Pierce). After blocking, the detection antibody(Goat anti-Rabbit HRP) was added and complexed with bound IgG. The platewas washed with 1×PBS containing 0.1% Tween 20 to remove excessdetection antibody. The NIR HRP substrate was then added in assay buffer(0.1M sodium citrate pH 4 with 0.1% Triton and 60 μM hydrogen peroxide).The plate was incubated at ambient temperature (FIG. 1).

Results showed that the intensity of the fluorescence signal increasedwith increasing concentration of Rabbit IgG. Since the fluorescenceresponse was dependent on the concentration of the Rabbit IgG, proof ofconcept for use of hydrocyanine dyes as HRP substrates was demonstrated.FIG. 2 shows an NIR HRP Substrate in Direct ELISA Assay Using Rabbit IgG(Antigen) and Goat Anti-Rabbit HRP Detection Antibody.

Example 12

Hydrocyanines: New tools to study effects of ROS in Hypoxia. Reactiveoxygen species (ROS), such as oxygen free radicals, play an exceedinglyimportant role in cancer cell response to growth factor signaling andhypoxia. Recent studies suggest that oxygen depletion stimulatesmitochondria to overproduce ROS, with subsequent activation of thetranscription factor hypoxia-inducible factor 1a (HIF1a), and thuspromoting cancer cell survival and tumor growth. Furthermore, asmitochondria plays a major role in the chemotherapy induced apoptosisinduction, the intricate relationships among mitochondria, ROS signalingand activation of survival pathways under hypoxic conditions have drawntremendous interests.

We present a number of near-infrared hydrocyanine probes as tools forimaging ROS for in vitro cell culture, ex vivo tissue section, and mostimportantly in vivo. Hydrocyanine probes are capable of detecting ROS influorescence microscope, fluorescence plate reader, flow cytometry andin vivo imaging platforms with high specificity and excellentsensitivity. There are several advantages for using hydrocyanine probesincluding 1) ease of use, 2) excellent sensitivity and specificity, 3)multiplexing assays with other cell health detection agents and 4)unprecedented flexibility in terms of imaging platforms and biologicalsystems. Near-infrared hydrocyanine probes therefore, can potentially beused to study the ROS mediated cell signaling pathways under hypoxicconditions.

Example 13

The following hydrocyanines and deuterocyanines were synthesized. Theirexcitation and emission wavelengths are suitable to be imaged in the 800channel.

DIR780F2-P: Two Hours at Ambient Temperature Trition X-100 pH 5 pH 6 (%)0.1 0.05 0.01 0.1 0.05 0.01 −Enzyme 14612 15268 15096 16995 14729 1788921194 15983 17026 16006 12646 15381 14653 14330 15697 16257 16731 1871319749 14897 14316 14644 12242 12600 +Enzyme 86168 78778 110308 116984111403 107251 73669 63411 71667 72420 65943 71002 79940 81063 9172095384 95434 93017 72029 67718 73540 65401 70952 72922 Mean 14716 1601117016 17956 15498 13218 Background Mean Signal 81487 103599 101776 6920770757 70205 Signal- 66771 87588 84761 51251 55259 56987 Background

A. Synthesis of IR 780F2

To an oven dried pressure tube with a magnetic stir-bar were addedIR-780 (400 mg, 0.74 mmol), 2,3-difluoro phenyl boronic acid (1.17 g,6.23 mmol), palladium (0) tetrakis (222 mg), 4.5 mL THF and 1.5 mLnano-pure water followed by 1.44 mL DIPEA. The reaction mixture wasflashed with N₂ and was heated to 115° C. for 2 h. Mass spectralanalysis indicated only the desired product with a very little peakcorresponding to the decholinated starting material (m/z=506). Theproduct was purified using Teledyne's Isco CombiFlash system usingdichloromethane/methanol as eluent.

IR-780-F2 (50 mg)+methanol (20 mL); turned a green clear solution. NaBD₄(10.2 mg) were added slowly. The solution turned bright yellow. Thereaction mixture was stirred @ RT for 15 min and the product formationand the disappearance of the starting material was observed in mass specanalysis. Silica gel (˜1 g) was added and the solvent was removed toobtain a yellow sample coated silica gel. The solid silica gel coatedreaction mixture was then loaded in the CombiFlash system and theproduct was purified using hexane/ethyl acetate as eluent. The massspectrometric results confirmed the product H-IR 780F2.

H-IR 780F2, H-IR 800 and D-IR 800 were synthesized following similarsynthetic procedure as described above.

B. 800 HRP Substrate

Their efficacies as 800 HRP substrates have been tested in the ELISAformat. The results with D-IR780F2 as the 800 HRP substrate are shown inFIG. 3.

C. NIR Chemifluorescent Substrates:

800 Chemifluorescent Substrates: The following 800 chemifluorescentsubstrates were designed.

The chemifluorescent substrate 1 was synthesized by a straightforwardfour-step synthetic procedure.

700 Chemifluorescent Substrates: The following 700 substrates weredesigned.

D. Imaging Reactive Oxygen Species (ROS):

Four hydrocyanines (H-Cy3, H-IR675, H-IR780, and H-IR780F2) weresynthesized by the reduction of the corresponding cyanine dyes. Thehydrocyanines were further tested for imaging lipopolysaccharides (LPS)induced ROS generation in RAW264.7 macrophages.

H-Cy3 (Table 1), H-IR675 (Table 1), H-IR780 and H-IR780F2 (Table 1) weretested to detect LPS-induced ROS generation in 96-well plate withOdyssey and also by fluorescence microscope. RAW264.7 cells beingtreated with LPS (either 0.1 μg/ml or 1 g/ml for 4 hours or 17 hours)was loaded with 5 μM hydrocyanines and was incubated for 30 min beforeimaging by fluorescence microscope.

Lipopolysaccharide (LPS) is one of the most powerful bacterial virulencefactors in terms of proinflammatory properties. Both H-Cy3 and H-IR780F2showed increased fluorescent intensity in the LPS treated cells comparedto the untreated cells.

LPS from many bacterial species will initiate acute inflammatoryresponses in mammals that are typical of the host reaction to tissueinjury or infection. Reactive Oxygen Species (ROS) detection wasperformed with H-Cy3 (A), wherein the microscope setting: DSRED(Ex545/30×, T750P; EM620/60M); Phase; 20× Load the dye for 2 hours thentreat cells for 30 minutes; and Reactive Oxygen Species (ROS) detectionwith H-IR780F2 (B), wherein the microscope setting: Cy7 (Ex710/75,DC760LP; EM810/90); Phase; 20× Load the dye for 2 hours then treat cellsfor 30 minutes.

Example 14 Synthesis of Hydrocyanines

H-IR650DIOL (i.e.,6-((E)-2-((2Z,4E)-3-bromo-5-(1-(6-hydroxyhexyl)-3,3-dimethylindolin-2-yl)penta-2,4-dien-1-ylidene)-3,3-dimethylindolin-1-yl)hexan-1-ol)was synthesized according to FIG. 5.

Synthesis of Indole Hexanol Quaternary Salt: To an oven dried 100-mLround bottom flask with stir bar and septum under N₂ were added2,3,3-trimethylindolenine (4.81 g, 30.21 mmol), followed by6-bromohexanol (7.09 g, 39.16 mmol) and diisopropylethylamine (1.93 g,15.10 mmol). The reaction mixture was heated at 80° C. for 16 hours. Thereaction mixture was triturated with 90 mL of diethyl ether to produce apowder. The powder was filtered away from the supernatant and washed3×30 mL with diethyl ether. The powder was dried under vacuum and 6.12 g(60% yield) was recovered.

Synthesis of 650 Diol: To an oven dried 50-mL pressure tube with stirbar were added Indole hexanol quaternary Salt (1.00 g, 2.94 mmol),followed by bromo Schiff base (0.64 g, 1.67 mmol), sodium acetate (0.49g, 5.97 mmol) and ethanol (10 mL). The reaction was purged with N₂,capped and heated at 100° C. for 30 minutes. Silica gel (5 g) was addedand the solvent was removed to obtain a blue sample coated silica gel.The solid silica gel coated reaction mixture was then loaded in theCombiFlash system and the product was purified using water/methanol aseluent. Blue/purple crystals were obtained (0.264 g, 22% yield) and massspectrometric analysis confirmed the product (633.5 m/z+, observed;633.3 m/z+, expected). ¹H-NMR (500 MHz, CD₃OD): δ 8.43 (d, J=13.3 Hz,2H), 7.58 (d, J=7.6 Hz, 2H), 7.47 (t, J=7.25 Hz, 2H), 7.42 (d, J=7.9 Hz,2H), 7.36 (t, J=7.6 Hz, 2H), 6.54 (d, J=13.2 Hz, 2H), 4.23 (t, J=7.26Hz, 4H), 3.58 (t, J=6.3 Hz, 4H), 1.92 (comp, 4H), 1.79 (s, 12H), 1.57(comp, 12H).

Synthesis of H-650 Diol: To an oven dried 50-mL round bottom flask wasadded the 650 diol (0.051 g, 71.37 μmol), followed by methanol (51 mL);turned a blue/purple solution. Sodium borohydride (0.0041 g, 108.4 μmol)was added. The solution changed to pale yellow. The reaction mixture wasstirred at room temperature for 15 minutes. Silica gel (2 g) was addedand the solvent was removed to obtain a yellow sample coated silica gel.The solid gel coated reaction mixture was then loaded in the CombiFlashsystem and the product was purified using hexane/ethyl acetate aseluent. A total of 0.0233 g (51.4% yield) were obtained and massspectrometric analysis confirmed the product (635.5 m/z+, observed;635.7 m/z+, expected).

Synthesis of H-IRDye® 800CW: To an oven dried 50-mL round bottom flaskwas added 800CW carboxylate (0.064 g, 58.66 μmol), followed by methanol(64 mL); turned a clear green solution. Sodium borohydride (0.0048 g,126.9 μmol) was added. The solution changed to bright yellow/orange. Thereaction mixture was stirred at room temperature for 15 minutes. Silicagel (2 g) was added and the solvent was removed to obtain ayellow/orange sample coated silica gel. The solid gel coated reactionmixture was then loaded in the CombiFlash system and the product waspurified using water/acetonitrile as eluent. A total of 0.0329 g (51.3%yield) were obtained and mass spectrometric analysis confirmed theproduct (1004.3 m/z+, observed; 1004.5 m/z+, expected). ¹H-NMR (500 MHz,D20): δ 7.78 (d, J=7.25, 2H), 7.58 (d, J=8.51, 1H), 7.51 (comp, 3H),7.42 (s, 1H), 7.19 (d, J=7.90, 2H), 6.8 (comp, 1H), 6.73 (comp, 2H),6.63 (d, J=8.51, 1H), 5.85 (dd, J=9.46, 1H), 5.55 (d, J=12.3, 1H), 3.75(comp, 4H), 3.11 (comp, 2H), 2.92 (comp, 4H), 2.59 (comp, 4H), 2.15(comp, 4H), 1.90 (comp, 2H), 1.68 (comp, 2H), 1.60 (comp, 2H), 1.57(comp, 2H), 1.49 (comp, 2H), 1.40 (comp, 2H), 1.34 (comp, 12H). See FIG.6.

Example 15 In Vitro ROS Detection with Hydrocyanines

ROS detection in LPS-treated RAW cells with H-IR650DIOL. Mousemacrophase cells, RAW 264.7, were treated with lipopolysaccharideendotoxin (LPS; 500 ng/mL) for 24 hrs prior to incubation withH-IR650DIOL (5 μM) for 30 min. Cells were imaged by fluorescencemicroscopy, as shown in FIG. 7 (microscope settings: Cy5 (1893 ms)(Ex620/60, DC660LP; EM7000/75); Phase (38 ms); 40×).

ROS detection in LPS treated RAW cells with H-IR680DIOL. Mousemacrophase cells, RAW 264.7, were treated with lipopolysaccharideendotoxin (LPS; 500 ng/mL) for 24 hrs prior to incubation withH-IR680DIOL (10 or 50 μM) for 30 min. Cells were imaged by fluorescencemicroscopy, as shown in FIG. 8 (microscope settings: Cy5 (140 ms)(Ex620/60, DC660LP; EM7000/75; Phase (100 ms); 40×).

ROS detection in LPS-treated RAW cells with H-Cy5. Mouse macrophasecells, RAW 264.7, were treated with lipopolysaccharide endotoxin (LPS;500 ng/mL) for 24 hrs prior to incubation with H-IR680DIOL (25 μM) for30 min. Cells were imaged by fluorescence microscopy, as shown in FIG. 9(microscope settings: Cy5 (1000 ms) (Ex620/60, DC660LP; EM700/75); Phase(50 ms); 20×).

ROS detection with H-IR675. Microscope setting: Cy6 (Ex620/60, DC660LP;EM700/75); Phase; 40×. Load the dye for 1 hours then treat cells for 30min. See FIG. 10.

Detection of hydrogen peroxide-induced ROS with H-Cy3. Mouse macrophagecells, RAW 264.7, were incubated with H-Cy3 (50 μM) for 2 hours followedby a 30 minute incubation with H₂O₂(1 mM). Cells were imaged byfluorescence microscopy using an Olympus IX81 inverted system microscope(20× phase), as shown in FIG. 11.

Detection of hydrogen peroxide-induced ROS with NIR probe H-IR780F2.Mouse macrophase cells, RAW 264.7, were incubated with Hydrocyanine-800(5 μM) for 1 hour followed by a 30 minute incubation with H₂O₂. Cellswere imaged by fluorescence microscopy using an using an Olympus IX81inverted system microscope (40× phase), as shown in FIG. 12.

Detection of EGF-induced ROS with NIR probe H-IR780F2. Human epithelialcarcinoma cells, A431, were incubated with Hydrocyanine-800 (50 uM,shown in green) for 2 hours followed by a 30 minute incubation with EGF.Cells were imaged by fluorescence microscopy using an using an OlympusIX81 inverted system microscope (40× phase), as shown in FIG. 13.

Example 16 In Vivo Analysis: Imaging of Implant-Induced ROS Production

Sterile, endotoxin-free PET disks (8 mm diameter) are implantedsubcutaneously following IACUC-approved procedures in 6- to 8-wk-oldmale BALB/c mice (Jackson Laboratories) anesthetized by isofluorane. Asingle 1-cm incision is made on the dorsum proximal to the spine, and asubcutaneous pocket laterally spanning the dorsum is created. Steriledisks (two per subject on either side of the spine) are implanted, andthe incision is closed using sterile wound clips. Mice undergoing thesame surgical procedure but receiving no biomaterial implants are usedas sham controls to account for surgery-associated trauma/inflammation.

For bioimaging, 30 μl of H-IRDye® 800CW at a concentration of 1 mg/ml insterile water is injected near the vicinity of the implant. Thirtyminutes after dye injection, the animal is anesthetized and the wholebody of the animal is scanned in an IVIS Lumina_bioimaging system(Xenogen). Biofluorescence is integrated using Living Image_softwareVersion 3.1 (Xenogen). ROS bioimaging is performed 30 min after dyeinjections immediately following surgery/implantation and 1, 4, 7 and 14days post-surgery/implantation.

H-IRDye 800 CW was also used for imaging.

On days 4 and 8 post-surgery, 50 ml of H-IR780F2 at a concentration of1.0 mg/ml in saline supplemented with 10% Cremophor EL and 10% DMSO isinjected into the jugular vein percutaneously. 10-15 minutes afterintravenous dye injections, the animals are scanned immediately in anIVIS Lumina_bioimaging system (Xenogen) and biofluorescence of imagingdata sets are acquired and quantified using Living Image_softwareVersion 3.1.

For additional material regarding a procedure, see Selvam et al. In VivoImaging of Biomaterial-Associated Inflammation at the Tissue-ImplantInterface, Biomaterials, 2011, 32, 7785-7792.

Example 17 Hydrocyanine and Deuterocyanine Dyes as ChemifluorescentProbes for Immunoassays

Detection of proteins in a complex biological sample with highsensitivity is playing an increasingly important role in understandingphysiological and pathological processes. The low relative abundance ofmany proteins within a biological sample and the limited quantity ofprecious sample make sensitive detection of target proteins highlydesirable in protein analysis. Chemiluminescence based detection hasbeen the method of choice for the Western blot and ELISA, but thesensitivity of the analysis is compromised as the accumulation of signalintensity is not possible in chemiluminescence. Here, we present a novelnear infrared chemifluorescent substrate, where the fluorescence signalwill accumulate with each turnover by the HRP enzyme and thus leadingunprecedented sensitivity.

Hydrocyanines, such as Hydro-IR780F2 or Deutero-IR780F2 are hydrophobicmolecules and will stick to a blotting membrane (e.g., a nitrocellulosemembrane), but they are non-fluorescent and will not emit light.Secondary antibody-HRP conjugates bound to protein bands on the membranewill oxidize the hydrocyanine or deuterocyanines to their parentfluorescent cyanine dye structure, however, and consequently the bandswill emit fluorescent signals. See FIG. 14. Because of the transientnature of the hydroxyl radical formed by the reaction of hydrogenperoxide and the antibody HRP conjugates, the radicals will oxidize onlythe hydro/deuterocyanines present in the close proximity to the proteinbands on the membrane and, therefore, the fluorescence signals will becompact. Furthermore, the oxidized fluorescent molecules are expected toaccumulate with each turn over by the HRP enzyme. The oxidized moleculeis also hydrophobic and therefore, is expected to stick to thehydrophobic membrane and hence, the sensitivity is expected to be betterthan chemiluminescence or secondary antibody detection methods.

In addition to hydro-IR780F2 and deutero-IR780F2, H-Cy5/D-Cy5(λ_(Ex)=640, λ_(Em)=660 nm) and H-Cy7/D-Cy7 (λ_(Ex)=740, λ_(Em)=760 nm)can be used for imaging in the NIR range while H-Cy3/D-Cy3 (λ_(Ex)=540,λ_(Em)=560 nm) can be used for the visible range.

Use of H-IR780F2 and H-IRDye® 800CW for blot imaging was compared to acommercially-available 680 HRP ELISA substrate (see FIG. 15). 4-12%Bis-Tris gels were loaded with 2-fold, 7-point serial dilutions of A431lysate (high conc.=2.0 rag), electrophoresed, transferred to OdysseyNitrocellulose, blocked with SeaBlock Blocking Buffer (with ProClinpreservative). The blots were probed with mouse anti-β actin antibodies,followed by HRP goat anti-mouse antibodies (FIG. 15, A-D) ordye-conjugated goat anti-mouse antibodies (FIG. 15, E-F). Blots probedwith HRP goat anti-mouse antibodies were incubated for 5 min withchemifluorescent substrates in buffer containing hydrogen peroxide.H-IRDye® 800CW and H-IR780F2 were tested at 10 μM with 50-200 μM H₂O₂.HRP 680 ELISA substrate was used according to published protocols (i.e.,LI-COR product no. 926-34300).

Observations: H-IRDye® 800CW substrate gave a “negative” signal withhigh background (FIG. 15A-B). H-IR780F2 resulted in good signal withhigh linearity for lower signals and moderate linearity for highersignals (FIG. 15C).

The chemifluorescent substrate H-IR780F2 (FIG. 16A-D) exhibits 32-foldsensitivity compared to chemiluminescent detection (using aluminol-based reagent system; FIG. 16D), and 16-fold sensitivitycompared to fluorescent dye-conjugated secondary antibody detection inWestern blots (FIG. 16E). Detection data for various probes issummarized in Table 2. The basic workflow remains unchanged andtherefore, the chemifluorescent substrate based analysis is amenable toother methods of protein analysis, such as ELISAs and protein arrays.

TABLE 2 Detection Limits for Luminescent/Fluorescent Probes Lower Limitof Detection Substrate Signal Type Detection (LLD) SuperSignal West Durachemiluminescence 62.5 ng (Thermo Scientific) IRDye 800CW- fluorescence31.3 ng goat anti-mouse conjugate H-IR780F2 chemifluorescence  1.5 ng

Example 18 Ratiometric Probe Hydrocyanine-560-Bodipy Probe

The ratiometric probe is synthesized by starting with cyanine-660:2EGand converting it to a mixed carbonate by treating withN,N′-Disuccinimidyl carbonate and diiospropylethyl amine (DIPEA). Themixed carbonate upon treatment with commercially available BODIPY Dyeamine forms cyanine-660:2EG-BODIPY. Reduction of cyanine-660:2EG-BODIPYwith sodium borohydride selectively reduces the imminium cation of thecyanine dye fragment leading to the corresponding ratiometrichydrocyanine probe (below). The excitation and emission wavelengths ofthe BODIPY dye and the cyanine-660 dye do not overlap.

Synthesis of Ratiometric Hydrocyanine-660:2EG-BODIPY

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

What is claimed is:
 1. A compound, wherein the compound has the formula:

wherein R^(1′) and R^(1a′) are each independently hydrogen or deuterium;M is an alkali metal cation; and R² is CO₂H or CO₂M.
 2. An assay methodfor measuring an analyte in a sample, the method comprising: a)contacting said sample with a binding reagent that binds to an analyteto form an analyte complex; b) contacting said sample with a compound ofclaim 1, wherein said compound reacts with a radical, wherein saidradical is generated from said analyte complex to form a detectableagent, which said detectable agent is a cyanine dye; and c) uponexcitation, detecting said detectable agent.
 3. The method of claim 2,wherein said analyte is a biological molecule.
 4. The method of claim 2,wherein said binding reagent is an antibody.
 5. The method of claim 2,wherein said analyte complex comprises an enzyme wherein a substrate ofthe enzyme is hydrogen peroxide.
 6. The method of claim 2, wherein saiddetectable agent is an oxidized form of a compound of claim
 1. 7. Themethod of claim 2, wherein said assay method is an immunologicaldetection method.
 8. The method of claim 7, wherein said immunologicaldetection method is a member selected from the group consisting of anenzyme linked immunosorbent assay (ELISA), a Western blot analysis, andan immunohistochemical analysis.
 9. A method for detecting a reactiveoxygen species in a cell of a sample or a subject, said methodcomprising: contacting a cell with one or more compounds of claim 1, toform an oxidized form of said compound; and exciting the oxidized formof said compound to emit light.
 10. The method of claim 9, wherein theoxidized form of said compound is detected by a method selected from thegroup consisting fluorescence spectroscopy or fluorescence microscopy.11. A kit for conducting a fluorescent assay, said kit comprising acomposition, said composition comprising: a) a compound of claim 1; andb) a buffer.
 12. The kit of claim 11, further comprising instructionsfor use of the composition in the fluorescent assay.